https://wiki.umiacs.umd.edu/cbcb/api.php?action=feedcontributions&feedformat=atom&user=Whitej Cbcb - User contributions [en] 2026-04-12T23:55:03Z User contributions MediaWiki 1.43.7 https://wiki.umiacs.umd.edu/cbcb/index.php?title=Cbcb:Pop-Lab:Papers&diff=4636 Cbcb:Pop-Lab:Papers 2009-02-19T16:29:13Z <p>Whitej: </p> <hr /> <div>== Metagenomics Reviews ==<br /> <br /> # V. Kunin, A. Copeland, A. Lapidues, K. Mavromatis and P. Hugenholtz. [http://mmbr.asm.org/cgi/reprint/72/4/557 A Bioinformatician's guide to Metagenomics].<br /> # Clarridge J.E. [http://cmr.asm.org/cgi/content/full/17/4/840#R62 16S sequencing and clinical microbiology review]<br /> # C. Riesenfield, P. Schloss, and J. Handelsman. [http://arjournals.annualreviews.org/doi/pdf/10.1146/annurev.genet.38.072902.091216 2004 Metagenomics review].<br /> # J. Eisen. [http://biology.plosjournals.org/perlserv/?request=get-document&amp;doi=10.1371/journal.pbio.0050082 Light metagenomics review for GOS expedition].<br /> <br /> == Pioneering papers ==<br /> <br /> # G Muyzer, E C de Waal and A G Uitterlinden [http://aem.asm.org/cgi/content/abstract/59/3/695 PCR amplifying 16S rRNA genes and DGGE]<br /> # D J Lane, B Pace, G J Olsen, D A Stahl, M L Sogin, and N R Pace [http://www.pnas.org/content/82/20/6955.abstract Rapid determination of 16S ribosomal RNA sequences for phylogenetic analyses]<br /> <br /> == 16S sequence analysis ==<br /> * ''Classification.''<br /> ** RDP classifier<br /> ** BLAST searches<br /> ** Multilocus classification<br /> ** Sogin-like database search methods<br /> ** Sanger ''vs.'' 454 <br /> * ''Alignment.''<br /> ** ClustalW<br /> ** NAST<br /> ** MUSCLE<br /> ** Pairwise<br /> ** Masking approaches (LaneMask)<br /> * ''Distance corrections.''<br /> ** Jukes-Cantor<br /> ** Kimura-2<br /> ** Felsenstein84<br /> ** Olsen<br /> * ''Clustering.''<br /> ** DOTUR<br /> ** VI-cut<br /> ** OTU picker (unpublished)<br /> ** Database versions (Sogin papers)<br /> * ''Community comparison.''<br /> ** Diversity estimators<br /> ** Rarefaction curves<br /> ** DOTUR<br /> ** EstimateS<br /> ** SONs<br /> ** TreeClimber<br /> ** S-libshuff<br /> ** UniFrac<br /> ** MEGAN<br /> ** Xipe - single sample comparisons<br /> ** Metastats</div> Whitej https://wiki.umiacs.umd.edu/cbcb/index.php?title=Cbcb:Pop-Lab:Papers&diff=4635 Cbcb:Pop-Lab:Papers 2009-02-19T16:21:58Z <p>Whitej: /* Pioneering papers */</p> <hr /> <div>== Metagenomics Reviews ==<br /> <br /> # V. Kunin, A. Copeland, A. Lapidues, K. Mavromatis and P. Hugenholtz. [http://mmbr.asm.org/cgi/reprint/72/4/557 A Bioinformatician's guide to Metagenomics].<br /> # Clarridge J.E. [http://cmr.asm.org/cgi/content/full/17/4/840#R62 16S sequencing and clinical microbiology review]<br /> # C. Riesenfield, P. Schloss, and J. Handelsman. [http://arjournals.annualreviews.org/doi/pdf/10.1146/annurev.genet.38.072902.091216 2004 Metagenomics review].<br /> # J. Eisen. [http://biology.plosjournals.org/perlserv/?request=get-document&amp;doi=10.1371/journal.pbio.0050082 Light metagenomics review for GOS expedition].<br /> <br /> == Pioneering papers ==<br /> <br /> # G Muyzer, E C de Waal and A G Uitterlinden [http://aem.asm.org/cgi/content/abstract/59/3/695 PCR amplifying 16S rRNA genes and DGGE]<br /> # D J Lane, B Pace, G J Olsen, D A Stahl, M L Sogin, and N R Pace [http://www.pnas.org/content/82/20/6955.abstract Rapid determination of 16S ribosomal RNA sequences for phylogenetic analyses]</div> Whitej https://wiki.umiacs.umd.edu/cbcb/index.php?title=Cbcb:Pop-Lab:Papers&diff=4634 Cbcb:Pop-Lab:Papers 2009-02-19T16:21:40Z <p>Whitej: /* Metagenomics Reviews */</p> <hr /> <div>== Metagenomics Reviews ==<br /> <br /> # V. Kunin, A. Copeland, A. Lapidues, K. Mavromatis and P. Hugenholtz. [http://mmbr.asm.org/cgi/reprint/72/4/557 A Bioinformatician's guide to Metagenomics].<br /> # Clarridge J.E. [http://cmr.asm.org/cgi/content/full/17/4/840#R62 16S sequencing and clinical microbiology review]<br /> # C. Riesenfield, P. Schloss, and J. Handelsman. [http://arjournals.annualreviews.org/doi/pdf/10.1146/annurev.genet.38.072902.091216 2004 Metagenomics review].<br /> # J. Eisen. [http://biology.plosjournals.org/perlserv/?request=get-document&amp;doi=10.1371/journal.pbio.0050082 Light metagenomics review for GOS expedition].<br /> <br /> == Pioneering papers ==<br /> <br /> # G Muyzer, E C de Waal and A G Uitterlinden [http://aem.asm.org/cgi/content/abstract/59/3/695| PCR amplifying 16S rRNA genes and DGGE]<br /> # D J Lane, B Pace, G J Olsen, D A Stahl, M L Sogin, and N R Pace [http://www.pnas.org/content/82/20/6955.abstract| Rapid determination of 16S ribosomal RNA sequences for phylogenetic analyses]</div> Whitej https://wiki.umiacs.umd.edu/cbcb/index.php?title=Cbcb:Pop-Lab:Papers&diff=4633 Cbcb:Pop-Lab:Papers 2009-02-19T16:20:18Z <p>Whitej: /* Metagenomics Reviews */</p> <hr /> <div>== Metagenomics Reviews ==<br /> <br /> # V. Kunin, A. Copeland, A. Lapidues, K. Mavromatis and P. Hugenholtz. [http://mmbr.asm.org/cgi/reprint/72/4/557| A Bioinformatician's guide to Metagenomics].<br /> # Clarridge J.E. [http://cmr.asm.org/cgi/content/full/17/4/840#R62| 16S sequencing and clinical microbiology review]<br /> # C. Riesenfield, P. Schloss, and J. Handelsman. [http://arjournals.annualreviews.org/doi/pdf/10.1146/annurev.genet.38.072902.091216| 2004 Metagenomics review].<br /> # J. Eisen. [http://biology.plosjournals.org/perlserv/?request=get-document&amp;doi=10.1371/journal.pbio.0050082| Light metagenomics review for GOS expedition].<br /> <br /> == Pioneering papers ==<br /> <br /> # G Muyzer, E C de Waal and A G Uitterlinden [http://aem.asm.org/cgi/content/abstract/59/3/695| PCR amplifying 16S rRNA genes and DGGE]<br /> # D J Lane, B Pace, G J Olsen, D A Stahl, M L Sogin, and N R Pace [http://www.pnas.org/content/82/20/6955.abstract| Rapid determination of 16S ribosomal RNA sequences for phylogenetic analyses]</div> Whitej https://wiki.umiacs.umd.edu/cbcb/index.php?title=Cbcb:Pop-Lab:Papers&diff=4632 Cbcb:Pop-Lab:Papers 2009-02-19T16:19:16Z <p>Whitej: /* Metagenomics Reviews */</p> <hr /> <div>== Metagenomics Reviews ==<br /> <br /> # V. Kunin, A. Copeland, A. Lapidues, K. Mavromatis and P. Hugenholtz. [http://mmbr.asm.org/cgi/reprint/72/4/557| A Bioinformatician's guide to Metagenomics].<br /> # Clarridge J.E. [http://cmr.asm.org/cgi/content/full/17/4/840#R62 | 16S sequencing and clinical microbiology review]<br /> # C. Riesenfield, P. Schloss, and J. Handelsman. [http://arjournals.annualreviews.org/doi/pdf/10.1146/annurev.genet.38.072902.091216 | 2004 Metagenomics review].<br /> # J. Eisen. [http://biology.plosjournals.org/perlserv/?request=get-document&amp;doi=10.1371/journal.pbio.0050082 | Light metagenomics review for GOS expedition].<br /> <br /> == Pioneering papers ==<br /> <br /> # G Muyzer, E C de Waal and A G Uitterlinden [http://aem.asm.org/cgi/content/abstract/59/3/695| PCR amplifying 16S rRNA genes and DGGE]<br /> # D J Lane, B Pace, G J Olsen, D A Stahl, M L Sogin, and N R Pace [http://www.pnas.org/content/82/20/6955.abstract| Rapid determination of 16S ribosomal RNA sequences for phylogenetic analyses]</div> Whitej https://wiki.umiacs.umd.edu/cbcb/index.php?title=Cbcb:Pop-Lab:Papers&diff=4631 Cbcb:Pop-Lab:Papers 2009-02-19T16:18:51Z <p>Whitej: /* Metagenomics Reviews */</p> <hr /> <div>== Metagenomics Reviews ==<br /> <br /> # V. Kunin, A. Copeland, A. Lapidues, K. Mavromatis and P. Hugenholtz. [http://mmbr.asm.org/cgi/reprint/72/4/557| A Bioinformatician's guide to Metagenomics].<br /> # Clarridge J.E. [http://cmr.asm.org/cgi/content/full/17/4/840#R62| 16S sequencing and clinical microbiology review]<br /> # C. Riesenfield, P. Schloss, and J. Handelsman. [http://arjournals.annualreviews.org/doi/pdf/10.1146/annurev.genet.38.072902.091216| 2004 Metagenomics review].<br /> # J. Eisen. [http://biology.plosjournals.org/perlserv/?request=get-document&amp;doi=10.1371/journal.pbio.0050082| Light metagenomics review for GOS expedition].<br /> <br /> == Pioneering papers ==<br /> <br /> # G Muyzer, E C de Waal and A G Uitterlinden [http://aem.asm.org/cgi/content/abstract/59/3/695| PCR amplifying 16S rRNA genes and DGGE]<br /> # D J Lane, B Pace, G J Olsen, D A Stahl, M L Sogin, and N R Pace [http://www.pnas.org/content/82/20/6955.abstract| Rapid determination of 16S ribosomal RNA sequences for phylogenetic analyses]</div> Whitej https://wiki.umiacs.umd.edu/cbcb/index.php?title=Cbcb:Pop-Lab:Papers&diff=4630 Cbcb:Pop-Lab:Papers 2009-02-19T16:14:27Z <p>Whitej: /* Metagenomics Reviews */</p> <hr /> <div>== Metagenomics Reviews ==<br /> <br /> # V. Kunin, A. Copeland, A. Lapidues, K. Mavromatis and P. Hugenholtz. [http://mmbr.asm.org/cgi/reprint/72/4/557| A Bioinformatician's guide to Metagenomics].<br /> # Clarridge J.E. [http://cmr.asm.org/cgi/content/full/17/4/840#R62| 16S sequencing and clinical microbiology review]<br /> # C. Riesenfield, P. Schloss, and J. Handelsman. [http://arjournals.annualreviews.org/doi/pdf/10.1146/annurev.genet.38.072902.091216| 2004 Metagenomics review].<br /> <br /> == Pioneering papers ==<br /> <br /> # G Muyzer, E C de Waal and A G Uitterlinden [http://aem.asm.org/cgi/content/abstract/59/3/695| PCR amplifying 16S rRNA genes and DGGE]<br /> # D J Lane, B Pace, G J Olsen, D A Stahl, M L Sogin, and N R Pace [http://www.pnas.org/content/82/20/6955.abstract| Rapid determination of 16S ribosomal RNA sequences for phylogenetic analyses]</div> Whitej https://wiki.umiacs.umd.edu/cbcb/index.php?title=Cbcb:Pop-Lab:Papers&diff=4629 Cbcb:Pop-Lab:Papers 2009-02-19T15:59:11Z <p>Whitej: /* Metagenomics Reviews */</p> <hr /> <div>== Metagenomics Reviews ==<br /> <br /> # V. Kunin, A. Copeland, A. Lapidues, K. Mavromatis and P. Hugenholtz. [http://mmbr.asm.org/cgi/reprint/72/4/557| A Bioinformatician's guide to Metagenomics].<br /> # Clarridge J.E. [http://cmr.asm.org/cgi/content/full/17/4/840#R62| 16S sequencing and clinical microbiology review]<br /> <br /> == Pioneering papers ==<br /> <br /> # G Muyzer, E C de Waal and A G Uitterlinden [http://aem.asm.org/cgi/content/abstract/59/3/695| PCR amplifying 16S rRNA genes and DGGE]<br /> # D J Lane, B Pace, G J Olsen, D A Stahl, M L Sogin, and N R Pace [http://www.pnas.org/content/82/20/6955.abstract| Rapid determination of 16S ribosomal RNA sequences for phylogenetic analyses]</div> Whitej https://wiki.umiacs.umd.edu/cbcb/index.php?title=Cbcb:Pop-Lab:James-Report&diff=4542 Cbcb:Pop-Lab:James-Report 2009-02-12T03:14:30Z <p>Whitej: </p> <hr /> <div>''Progress reports:''<br /> <br /> * [[February]]</div> Whitej https://wiki.umiacs.umd.edu/cbcb/index.php?title=Cbcb:Pop-Lab:James-Report&diff=4541 Cbcb:Pop-Lab:James-Report 2009-02-12T03:13:16Z <p>Whitej: </p> <hr /> <div>''Progress reports:''<br /> February</div> Whitej https://wiki.umiacs.umd.edu/cbcb/index.php?title=Cbcb:Pop-Lab&diff=4540 Cbcb:Pop-Lab 2009-02-12T03:12:07Z <p>Whitej: </p> <hr /> <div>= Important pages =<br /> * Group members [[Cbcb:Pop-Lab:Members]] <br /> * Blog: [http://genomes.blogspot.com Genomes.blogspot.com]<br /> * How-tos: [[Cbcb:Pop-Lab:How-to]] - List of documentation on how to perform certain analyses, use different software, etc.<br /> * Software developed by us: [[Cbcb:Pop-Lab:Software]]<br /> <br /> = Meetings/seminars =<br /> * [[Pop_group_meeting|Group meeting]]: every Monday from 2:30pm in corner conference room (3120 C)<br /> * [[seminars|CBCB seminar]]: Thursdays 2-3pm during the semester in main conference room<br /> <br /> = Progress Reports =<br /> * [[Cbcb:Pop-Lab:Niranjan-Report|Niranjan]]<br /> * [[Cbcb:Pop-Lab:Chris-Report|Chris]]<br /> * [[Cbcb:Pop-Lab:James-Report|James]]<br /> <br /> = Pop Lab Presentations =<br /> * [[Media:Xoo_Cripsr.odg|Xanthomonas Crispr Slides (openoffice format)]] <br /> * Listeria Monocytogenes Slides (powerpoint)<br /> * Metagenome pipelines overview [[Media:Pipeline_outline.pdf|Presentation(pdf)]]</div> Whitej https://wiki.umiacs.umd.edu/cbcb/index.php?title=Cbcb:Pop-Lab:OTUs_How_do_I_create_OTUs_from_16S_rRNA_sequence_data%3F&diff=4261 Cbcb:Pop-Lab:OTUs How do I create OTUs from 16S rRNA sequence data? 2009-01-06T20:13:40Z <p>Whitej: </p> <hr /> <div>james robert white, whitej@umd.edu &lt;br&gt;<br /> &lt;br&gt;<br /> To begin:&lt;br&gt;<br /> You need a fasta file of 16S sequences.&lt;br&gt;<br /> &lt;br&gt;<br /> 1. Make sure all sequences are in the correct orientation. You may need to reverse complement several.&lt;br&gt;<br /> 2. Perform a multiple sequence alignment. This can be done using several programs such as ClustalW, MUSCLE, NAST, or MAFFT.&lt;br&gt;<br /> Each MSA program has options for outputting an alignment in different formats (e.g. FASTA, ClustalW, PHYLIP)&lt;br&gt;<br /> 4. Trim the MSA so that each sequence spans the entire alignment. You may need to remove poor sequences altogether.&lt;br&gt; <br /> 5. Create a distance matrix from your MSA. A matrix must include an evolutionary distance correction such as Jukes-Cantor or Olsen. This can be done several ways:&lt;br&gt;<br /> *DNADIST from the PHYLIP package. (Jukes-Cantor, Kimura-2, or Felsenstein 84 corrections) &lt;br&gt;<br /> *ARB has functions for loading an MSA and creating distance matrices. (Jukes-Cantor, Felsenstein 84,and Olsen corrections) &lt;br&gt; <br /> The distance matrix will be in one of two formats: square or lower triangular. Be sure to know which one you have.&lt;br&gt;<br /> 6. The distance matrix serves as input to an OTU program such as DOTUR. DOTUR clusters sequences in OTU according to their relative distances. The default clustering algorithm is complete linkage (furthest neighbor) &lt;br&gt;<br /> 7. A large number of files are created by DOTUR, but the following are most important:&lt;br&gt;<br /> * *.list - the actual list of OTUs. Each line is tab delimited. The first element is the distance threshold, the 2nd element is the number of OTUs, and all subsequent elements are the individual OTUs. Members of each OTU are delimited by commas.&lt;br&gt; <br /> * *ace.ltt - ACE diversity estimates for different thresholds. &lt;br&gt;<br /> * *chao.ltt - CHAO1 diversity estimates for different thresholds. &lt;br&gt;<br /> * *shannon.ltt - Shannon diversity estimates for different thresholds. &lt;br&gt;<br /> &lt;br&gt;</div> Whitej https://wiki.umiacs.umd.edu/cbcb/index.php?title=Cbcb:Pop-Lab:OTUs_How_do_I_create_OTUs_from_16S_rRNA_sequence_data%3F&diff=4260 Cbcb:Pop-Lab:OTUs How do I create OTUs from 16S rRNA sequence data? 2009-01-06T20:11:51Z <p>Whitej: </p> <hr /> <div>james robert white, whitej@umd.edu &lt;br&gt;<br /> &lt;br&gt;<br /> To begin:&lt;br&gt;<br /> You need a fasta file of 16S sequences.&lt;br&gt;<br /> &lt;br&gt;<br /> 1. Make sure all sequences are in the correct orientation. You may need to reverse complement several.&lt;br&gt;<br /> 2. Perform a multiple sequence alignment. This can be done using several programs such as ClustalW, MUSCLE, NAST, or MAFFT.&lt;br&gt;<br /> Each MSA program has options for outputting an alignment in different formats (e.g. FASTA, ClustalW, PHYLIP)&lt;br&gt;<br /> 4. Trim the MSA so that each sequence spans the entire alignment. You may need to remove poor sequences altogether.&lt;br&gt; <br /> 5. Create a distance matrix from your MSA. A matrix must include an evolutionary distance correction such as Jukes-Cantor or Olsen. This can be done several ways:&lt;br&gt;<br /> (i) DNADIST from the PHYLIP package. (Jukes-Cantor, Kimura-2, or Felsenstein 84 corrections) &lt;br&gt;<br /> (ii) ARB has functions for loading an MSA and creating distance matrices. (Jukes-Cantor, Felsenstein 84,and Olsen corrections) &lt;br&gt; <br /> The distance matrix will be in one of two formats: square or lower triangular. Be sure to know which one you have.&lt;br&gt;<br /> 6. The distance matrix serves as input to an OTU program such as DOTUR. DOTUR clusters sequences in OTU according to their relative distances. The default clustering algorithm is complete linkage (furthest neighbor) &lt;br&gt;<br /> 7. A large number of files are created by DOTUR, but the following are most important:&lt;br&gt;<br /> (i) *.list - the actual list of OTUs. Each line is tab delimited. The first element is the distance threshold, the 2nd element is the number of OTUs, and all subsequent elements are the individual OTUs. Members of each OTU are delimited by commas.&lt;br&gt; <br /> (ii) *ace.ltt - ACE diversity estimates for different thresholds. &lt;br&gt;<br /> (iii) *chao.ltt - CHAO1 diversity estimates for different thresholds. &lt;br&gt;<br /> (iv) *shannon.ltt - Shannon diversity estimates for different thresholds. &lt;br&gt;<br /> &lt;br&gt;</div> Whitej https://wiki.umiacs.umd.edu/cbcb/index.php?title=Cbcb:Pop-Lab:How-to&diff=4259 Cbcb:Pop-Lab:How-to 2009-01-06T20:00:09Z <p>Whitej: /* How-To repository */</p> <hr /> <div>==How-To repository==<br /> [http://www.cbcb.umd.edu/intranet/resources.shtml Getting started at the CBCB] &lt;br&gt;<br /> [[Cbcb:Pop-Lab:AMOS-CVS How to use AMOS through CVS]] &lt;br&gt;<br /> [[Cbcb:Pop-Lab:AMOScmp-SR How to use AMOScmp with short read data ]] &lt;br&gt;<br /> How do I annotate a genome at the CBCB?&lt;br&gt;<br /> [[Cbcb:Pop-Lab:How do I run the new Bambus | How do I run the new Bambus?]] &lt;br&gt;<br /> How do I use the antibiotic resistance database?&lt;br&gt;<br /> How do I use the antibiotic resistance database locally? &lt;br&gt;<br /> How do I run jobs on the grid? &lt;br&gt;<br /> [[Cbcb:Pop-Lab:OTUs How do I create OTUs from 16S rRNA sequence data? | How do I create OTUs from 16S rRNA sequence data?]] &lt;br&gt;<br /> How do I compare metagenomic datasets through the metastats website?&lt;br&gt;<br /> How do I compare metagenomic datasets using R directly? &lt;br&gt;<br /> How do I find CRISPRs in a new genome?&lt;br&gt;<br /> [[Cbcb:Pop-Lab:SOMA How do I scaffold a genome using optical maps (both locally and through the web) ]] &lt;br&gt;<br /> How do I generate graph information out of Minimus?&lt;br&gt;<br /> What tools are available for doing &lt;i&gt;in silico&lt;/i&gt; finishing at the CBCB? &lt;br&gt;<br /> How do I generate a scaffold graph starting from a 454 .ace file?&lt;br&gt;<br /> How do I draw a pretty picture of a scaffold stored in an AMOS bank?&lt;br&gt;</div> Whitej https://wiki.umiacs.umd.edu/cbcb/index.php?title=Cbcb:Pop-Lab:OTUs_How_do_I_create_OTUs_from_16S_rRNA_sequence_data%3F&diff=4258 Cbcb:Pop-Lab:OTUs How do I create OTUs from 16S rRNA sequence data? 2009-01-06T19:58:13Z <p>Whitej: </p> <hr /> <div>'''How do I create OTUs from 16S sequence data?''' &lt;br&gt;<br /> james robert white, whitej@umd.edu &lt;br&gt;<br /> &lt;br&gt;<br /> To begin:&lt;br&gt;<br /> You need a fasta file of 16S sequences.&lt;br&gt;<br /> 1. Make sure all sequences are in the correct orientation. You may need to reverse complement several.&lt;br&gt;<br /> 2. Perform a multiple sequence alignment. This can be done using several programs such as ClustalW, MUSCLE, NAST, or MAFFT.&lt;br&gt;<br /> Each MSA program has options for outputting an alignment in different formats (e.g. FASTA, ClustalW, PHYLIP)&lt;br&gt;<br /> 3. Create a distance matrix from your MSA.&lt;br&gt;<br /> &lt;br&gt;</div> Whitej https://wiki.umiacs.umd.edu/cbcb/index.php?title=Cbcb:Pop-Lab:OTUs_How_do_I_create_OTUs_from_16S_rRNA_sequence_data%3F&diff=4257 Cbcb:Pop-Lab:OTUs How do I create OTUs from 16S rRNA sequence data? 2009-01-06T19:57:19Z <p>Whitej: Created a page for OTU creation. needs work.</p> <hr /> <div>'''How do I create OTUs from 16S sequence data?'''<br /> james robert white, whitej@umd.edu<br /> <br /> To begin:<br /> You need a fasta file of 16S sequences.<br /> 1. Make sure all sequences are in the correct orientation. You may need to reverse complement several.<br /> 2. Perform a multiple sequence alignment. This can be done using several programs such as ClustalW, MUSCLE, NAST, or MAFFT.<br /> Each MSA program has options for outputting an alignment in different formats (e.g. FASTA, ClustalW, PHYLIP)<br /> 3. Create a distance matrix from your MSA.</div> Whitej https://wiki.umiacs.umd.edu/cbcb/index.php?title=Cbcb:Pop-Lab:How-to&diff=4256 Cbcb:Pop-Lab:How-to 2009-01-06T19:52:26Z <p>Whitej: added OTU pages</p> <hr /> <div>==How-To repository==<br /> [http://www.cbcb.umd.edu/intranet/resources.shtml Getting started at the CBCB] &lt;br&gt;<br /> [[Cbcb:Pop-Lab:AMOS-CVS How to use AMOS through CVS]] &lt;br&gt;<br /> [[Cbcb:Pop-Lab:AMOScmp-SR How to use AMOScmp with short read data ]] &lt;br&gt;<br /> How do I annotate a genome at the CBCB?&lt;br&gt;<br /> [[Cbcb:Pop-Lab:How do I run the new Bambus | How do I run the new Bambus?]] &lt;br&gt;<br /> How do I use the antibiotic resistance database?&lt;br&gt;<br /> How do I use the antibiotic resistance database locally? &lt;br&gt;<br /> How do I run jobs on the grid? &lt;br&gt;<br /> [[Cbcb:Pop-Lab:OTUs How do I create OTUs from 16S rRNA sequence data?]] &lt;br&gt;<br /> How do I compare metagenomic datasets through the metastats website?&lt;br&gt;<br /> How do I compare metagenomic datasets using R directly? &lt;br&gt;<br /> How do I find CRISPRs in a new genome?&lt;br&gt;<br /> [[Cbcb:Pop-Lab:SOMA How do I scaffold a genome using optical maps (both locally and through the web) ]] &lt;br&gt;<br /> How do I generate graph information out of Minimus?&lt;br&gt;<br /> What tools are available for doing &lt;i&gt;in silico&lt;/i&gt; finishing at the CBCB? &lt;br&gt;<br /> How do I generate a scaffold graph starting from a 454 .ace file?&lt;br&gt;<br /> How do I draw a pretty picture of a scaffold stored in an AMOS bank?&lt;br&gt;</div> Whitej https://wiki.umiacs.umd.edu/cbcb/index.php?title=Pop_group_meeting&diff=3937 Pop group meeting 2008-11-24T16:59:01Z <p>Whitej: /* 11/17/2008 */</p> <hr /> <div>= 09/29/2008 =<br /> <br /> # Benjamin Langmead [http://www.plosone.org/article/info:doi%2F10.1371%2Fjournal.pone.0003263 Metagenomic Analysis of Lysogeny in Tampa Bay: Implications for Prophage Gene Expression] (PLoS one)<br /> # Bo Liu [http://genomebiology.com/2008/9/9/R139 Systematic bioinformatic analysis of expression levels of 17,330 human genes across 9,783 samples from 175 types of healthy and pathological tissues] (Genome Biology)<br /> # Daniela Puiu [http://genome.cshlp.org/cgi/reprint/gr.080200.108v1 Sequencing of natural strains of Arabidopsis thaliana with short reads] (Genome Research)<br /> # Dan Sommer, Niranjan Nagarajan [http://www.nature.com/nature/journal/v455/n7212/edsumm/e080925-04.html Metagenomics: questions to answer] (Nature)<br /> # James Robert White [http://www.sciencedirect.com/science?_ob=ArticleURL&amp;_udi=B6V73-4SHVST0-1&amp;_user=961305&amp;_rdoc=1&amp;_fmt=&amp;_orig=search&amp;_sort=d&amp;view=c&amp;_version=1&amp;_urlVersion=0&amp;_userid=961305&amp;md5=4115e7b8186a36db60f6b11a217a8798 Microbial population dynamics during aerobic sludge granulation at different organic loading rates] (ScienceDirect)<br /> # Mohammad Reza Ghodsi [http://nar.oxfordjournals.org/cgi/content/short/36/16/5180 A comparison of random sequence reads versus 16S rDNA sequences for estimating the biodiversity of a metagenomic library] (NAR)<br /> # Sergey Koren [http://www.biomedcentral.com/1471-2105/9/390 R/parallel - speeding up bioinformatics analysis with R] (BMC Bioinformatics)<br /> # Theodore Gibbons [http://www.ncbi.nlm.nih.gov/pubmed/18711340 High-resolution metagenomics targets specific functional types in complex microbial communities] (Nature Biotechnology) &lt;BR&gt; [http://www.nature.com/nrmicro/journal/v6/n9/abs/nrmicro1935.html Molecular eco-systems biology: towards an understanding of community function] (Systems Microbiology)<br /> <br /> = 10/06/2008 =<br /> # Bo Liu [http://www.pnas.org/content/105/39/15076.short The convergence of carbohydrate active gene repertoires in human gut microbes.] PNAS<br /> # Daniela Puiu [http://bioinformatics.oxfordjournals.org/cgi/content/full/24/20/2395 SeqMap: mapping massive amount of oligonucleotides to the genome] Bioinformatics<br /> # James Robert White [http://www.pnas.org/content/104/21/8918.full Artificial selection of simulated microbial ecosystems.] PNAS<br /> # MohammadReza Ghodsi [http://aem.asm.org/cgi/content/abstract/74/5/1453 Metagenomics: Read Length Matters] Applied Environmental Microbiology<br /> # Sergey Koren [http://www.ploscompbiol.org/article/info:doi%2F10.1371%2Fjournal.pcbi.1000186 Gene-Boosted Assembly of a Novel Bacterial Genome from Very Short Reads] PLoS Computational Biology<br /> <br /> = 10/13/2008 =<br /> # Daniela Puiu, Daniel Sommer [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0003373 MetaSim—A Sequencing Simulator for Genomics and Metagenomics] PLoS ONE<br /> # Bo Liu, James Robert White [http://www.sciencemag.org/cgi/content/full/322/5899/275 Environmental Genomics Reveals a Single-Species Ecosystem Deep Within Earth.] Science<br /> # MohammadReza Ghodsi [http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2557142 Probing Metagenomics by Rapid Cluster Analysis of Very Large Datasets] (PLoS one)<br /> <br /> MetaSim software:<br /> Location: /fs/sz-user-supported/common/packages/MetaSim/ <br /> Executable(Java): /fs/sz-user-supported/common/packages/MetaSim/metasim/MetaSim <br /> Database: /fs/sz-user-supported/common/packages/MetaSim/database <br /> create a symlink to it from your working directory, otherwise you have to import it <br /> NCBI databases: [ftp://ftp.ncbi.nlm.nih.gov/genomes/Bacteria/all.fna.tar.gz Complete bacteria]; [ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/gi_taxid_nucl.dmp.gz Taxonomy]<br /> <br /> = 10/20/2008 =<br /> # Bo Liu [http://www.pnas.org/content/105/37/13977.short?rss=1 Accelerated evolution of resistance in multidrug environments] PNAS &lt;br&gt; [http://www.pnas.org/content/105/39/14918.short?rss=1 Drug interactions modulate the potential for evolution of resistance] PNAS<br /> # Daniel Sommer [http://www.ncbi.nlm.nih.gov/pubmed/18927115?dopt=Abstract NCBI Reference Sequences: current status, policy and new initiatives] NAR<br /> # Daniela Puiu [http://genomebiology.com/content/pdf/gb-2008-9-10-r151.pdf A simple, fast, and accurate method of phylogenomic inference] Genome Biology<br /> # Niranjan Nagarajan [http://www.springerlink.com/content/cn3551154w232l73/fulltext.pdf The Stastical Power of Phylogenetic Motif Models] RECOMB 2008<br /> # Sergey Koren [http://www.nature.com/nmeth/journal/v5/n10/full/nmeth1008-903.html Scientific software: seeing the SNPs between us] Nature Methods<br /> # Mohammadreza Ghodsi [http://www.biomedcentral.com/1471-2105/9/386 The metagenomics RAST server – a public resource for the automatic phylogenetic and functional analysis of metagenomes] BMC Bioinformatics<br /> <br /> = 10/27/2008 =<br /> # Bo Liu [http://www.pnas.org/content/105/37/14130.short?rss=1 Frequent emergence and limited geographic dispersal of methicillin-resistant Staphylococcus aureus] PNAS<br /> # Sergey Koren [http://bioinformatics.oxfordjournals.org/cgi/content/abstract/btn548 Aggressive Assembly of Pyrosequencing Reads with Mates] Bioinformatics<br /> # Daniela Puiu [http://bioinformatics.oxfordjournals.org/cgi/content/full/24/21/2431 ZOOM! Zillions of oligos mapped] Bioinformatics<br /> # Mohammadreza Ghodsi [http://www.ncbi.nlm.nih.gov/pubmed/18692931 Biodiversity of the microbial community in a Spanish farmhouse cheese as revealed by culture-dependent and culture-independent methods]<br /> <br /> = 11/03/2008 = <br /> # Daniela Puiu [http://genome.cshlp.org/cgi/content/abstract/gr.7088808v1 Short read fragment assembly of bacterial genomes] (Genome Research)<br /> <br /> = 11/10/2008 = <br /> # Bo Liu [http://www.pnas.org/content/early/2008/11/04/0802782105.abstract Metagenome analysis of an extreme microbial symbiosis reveals eurythermal adaptation and metabolic flexibility] PNAS<br /> <br /> = 11/17/2008 =<br /> # Bo Liu [http://bioinformatics.oxfordjournals.org/cgi/content/short/24/22/2579?rss=1 Phylogenetic distances are encoded in networks of interacting pathways] Bioinformatics<br /> # Daniela Puiu [http://bioinformatics.oxfordjournals.org/cgi/content/abstract/btn582 Human genomes as email attachments] Bioinformatics<br /> # Mohammad Ghodsi [http://nar.oxfordjournals.org/cgi/content/short/36/18/e120 Accurate taxonomy assignments from 16S rRNA sequences produced by highly parallel pyrosequencers] Nucleic Acids Research<br /> # Sergey Koren [http://www.biomedcentral.com/1471-2105/9/420/abstract XplorSeq: A software environment for integrated management and phylogenetic analysis of metagenomic sequence data] (BMC Bioinformatics)<br /> # James Robert White [http://www.pnas.org/content/early/2008/08/08/0801925105.abstract?etoc Resistance, resilience, and redundancy in microbial communities] PNAS</div> Whitej https://wiki.umiacs.umd.edu/cbcb/index.php?title=Pop_group_meeting&diff=3590 Pop group meeting 2008-10-13T18:54:19Z <p>Whitej: </p> <hr /> <div>= 09/29/2008 =<br /> <br /> # Benjamin Langmead [http://www.plosone.org/article/info:doi%2F10.1371%2Fjournal.pone.0003263 Metagenomic Analysis of Lysogeny in Tampa Bay: Implications for Prophage Gene Expression] (PLoS one)<br /> # Bo Liu [http://genomebiology.com/2008/9/9/R139 Systematic bioinformatic analysis of expression levels of 17,330 human genes across 9,783 samples from 175 types of healthy and pathological tissues] (Genome Biology)<br /> # Daniela Puiu [http://genome.cshlp.org/cgi/reprint/gr.080200.108v1 Sequencing of natural strains of Arabidopsis thaliana with short reads] (Genome Research)<br /> # Dan Sommer [http://www.nature.com/nature/journal/v455/n7212/edsumm/e080925-04.html Metagenomics: questions to answer] (Nature)<br /> # James Robert White [http://www.sciencedirect.com/science?_ob=ArticleURL&amp;_udi=B6V73-4SHVST0-1&amp;_user=961305&amp;_rdoc=1&amp;_fmt=&amp;_orig=search&amp;_sort=d&amp;view=c&amp;_version=1&amp;_urlVersion=0&amp;_userid=961305&amp;md5=4115e7b8186a36db60f6b11a217a8798 Microbial population dynamics during aerobic sludge granulation at different organic loading rates] (ScienceDirect)<br /> # Mohammad Reza Ghodsi [http://nar.oxfordjournals.org/cgi/content/short/36/16/5180 A comparison of random sequence reads versus 16S rDNA sequences for estimating the biodiversity of a metagenomic library] (NAR)<br /> # Niranjan Nagarajan [http://www.nature.com/nature/journal/v455/n7212/edsumm/e080925-04.html Metagenomics: questions to answer] (Nature)<br /> # Sergey Koren [http://www.biomedcentral.com/1471-2105/9/390 R/parallel - speeding up bioinformatics analysis with R] (BMC Bioinformatics)<br /> # Theodore Gibbons [http://www.ncbi.nlm.nih.gov/pubmed/18711340 High-resolution metagenomics targets specific functional types in complex microbial communities] (Nature Biotechnology) &lt;BR&gt; [http://www.nature.com/nrmicro/journal/v6/n9/abs/nrmicro1935.html Molecular eco-systems biology: towards an understanding of community function] (Systems Microbiology)<br /> <br /> = 10/06/2008 =<br /> # Bo Liu [http://www.pnas.org/content/105/39/15076.short The convergence of carbohydrate active gene repertoires in human gut microbes.] PNAS<br /> # Daniela Puiu [http://bioinformatics.oxfordjournals.org/cgi/content/full/24/20/2395 SeqMap: mapping massive amount of oligonucleotides to the genome] Bioinformatics<br /> # James Robert White [http://www.pnas.org/content/104/21/8918.full Artificial selection of simulated microbial ecosystems.] PNAS<br /> # MohammadReza Ghodsi [http://aem.asm.org/cgi/content/abstract/74/5/1453 Metagenomics: Read Length Matters] Applied Environmental Microbiology<br /> <br /> = 10/13/2008 =<br /> # Daniela Puiu<br /> # Bo Liu &amp; James Robert White [http://www.sciencemag.org/cgi/content/full/322/5899/275 Environmental Genomics Reveals a Single-Species Ecosystem Deep Within Earth.] Science</div> Whitej https://wiki.umiacs.umd.edu/cbcb/index.php?title=Pop_group_meeting&diff=3516 Pop group meeting 2008-10-06T22:40:48Z <p>Whitej: /* 10/06/2008 */</p> <hr /> <div>= 09/29/2008 =<br /> <br /> # Benjamin Langmead [http://www.plosone.org/article/info:doi%2F10.1371%2Fjournal.pone.0003263 Metagenomic Analysis of Lysogeny in Tampa Bay: Implications for Prophage Gene Expression] (PLoS one)<br /> # Bo Liu [http://genomebiology.com/2008/9/9/R139 Systematic bioinformatic analysis of expression levels of 17,330 human genes across 9,783 samples from 175 types of healthy and pathological tissues] (Genome Biology)<br /> # Daniela Puiu [http://genome.cshlp.org/cgi/reprint/gr.080200.108v1 Sequencing of natural strains of Arabidopsis thaliana with short reads] (Genome Research)<br /> # Dan Sommer [http://www.nature.com/nature/journal/v455/n7212/edsumm/e080925-04.html Metagenomics: questions to answer] (Nature)<br /> # James Robert White [http://www.sciencedirect.com/science?_ob=ArticleURL&amp;_udi=B6V73-4SHVST0-1&amp;_user=961305&amp;_rdoc=1&amp;_fmt=&amp;_orig=search&amp;_sort=d&amp;view=c&amp;_version=1&amp;_urlVersion=0&amp;_userid=961305&amp;md5=4115e7b8186a36db60f6b11a217a8798 Microbial population dynamics during aerobic sludge granulation at different organic loading rates] (ScienceDirect)<br /> # Mohammad Reza Ghodsi [http://nar.oxfordjournals.org/cgi/content/short/36/16/5180 A comparison of random sequence reads versus 16S rDNA sequences for estimating the biodiversity of a metagenomic library] (NAR)<br /> # Niranjan Nagarajan [http://www.nature.com/nature/journal/v455/n7212/edsumm/e080925-04.html Metagenomics: questions to answer] (Nature)<br /> # Sergey Koren [http://www.biomedcentral.com/1471-2105/9/390 R/parallel - speeding up bioinformatics analysis with R] (BMC Bioinformatics)<br /> # Theodore Gibbons [http://www.ncbi.nlm.nih.gov/pubmed/18711340 High-resolution metagenomics targets specific functional types in complex microbial communities] (Nature Biotechnology) &lt;BR&gt; [http://www.nature.com/nrmicro/journal/v6/n9/abs/nrmicro1935.html Molecular eco-systems biology: towards an understanding of community function] (Systems Microbiology)<br /> <br /> = 10/06/2008 =<br /> # Daniela Puiu [http://bioinformatics.oxfordjournals.org/cgi/content/full/24/20/2395 SeqMap: mapping massive amount of oligonucleotides to the genome] Bioinformatics<br /> # James Robert White [http://www.pnas.org/content/104/21/8918.full Artificial selection of simulated microbial ecosystems.] PNAS</div> Whitej https://wiki.umiacs.umd.edu/cbcb/index.php?title=User:Whitej&diff=3333 User:Whitej 2008-09-09T18:24:18Z <p>Whitej: </p> <hr /> <div>James Robert White<br /> PhD student in Applied Mathematics, Scientific Computation<br /> <br /> * [http://www.cbcb.umd.edu/~whitej my webpage]</div> Whitej https://wiki.umiacs.umd.edu/cbcb/index.php?title=User:Whitej&diff=3332 User:Whitej 2008-09-09T18:22:58Z <p>Whitej: </p> <hr /> <div>James Robert White<br /> PhD student in Applied Mathematics, Scientific Computation<br /> <br /> * [[www.cbcb.umd.edu/~whitej|my webpage]]</div> Whitej https://wiki.umiacs.umd.edu/cbcb/index.php?title=Main_Page&diff=3331 Main Page 2008-09-09T18:20:50Z <p>Whitej: /* People */</p> <hr /> <div>== Seminars ==<br /> * [http://www.cbcb.umd.edu/seminars Regular CBCB seminars (during academic year)] &lt;br&gt;<br /> * [[Cbcb:Works-In-Progress]] - Works in progress seminar schedule (Summer 2008) &lt;br&gt;<br /> * [[short_read_sequencing|Short read sequencing Meeting]] (Fridays at 3pm)<br /> <br /> == Projects ==<br /> <br /> * [[Project:Pop-Lab|Pop-Lab]]<br /> <br /> == People ==<br /> <br /> * [[User:pknut777|Adam Lee Bazinet]] <br /> * [[User:amp|Adam M Phillipy]] <br /> * [[User:adelcher|Arthur L. Delcher]] <br /> * [[User:carlk|Carl Kinsford]] <br /> * [[User:dpuiu|Daniela Puiu]] <br /> * [[User:dsommer|Dan Sommer]] <br /> * [[User:gpertea|Geo Pertea]] <br /> * [[User:jeallen|Jonathan Edward All]] <br /> * [[User:ayanbule|Kunmi Ayanbule]] <br /> * [[User:conte|Matthew Conte]] <br /> * [[User:mschatz|Michael Schatz]] <br /> * [[User:mpertea|Mihaela Pertea]] <br /> * [[User:mpop|Mihai Pop]] <br /> * [[User:nelsayed|Najib El-Sayed]] <br /> * [[User:nedwards|Nathan Edwards]] <br /> * [[User:angiuoli|Samuel V Angluoli]] <br /> * [[User:salzberg|Steven Salzberg]]<br /> *[[User:whitej|James Robert White]]<br /> <br /> == Getting started ==<br /> <br /> * [http://www.mediawiki.org/wiki/Help:Configuration_settings Configuration settings list]<br /> * [http://www.mediawiki.org/wiki/Help:FAQ MediaWiki FAQ]<br /> * [http://mail.wikimedia.org/mailman/listinfo/mediawiki-announce MediaWiki release mailing list]</div> Whitej