User:Dpuiu

Daniela Puiu's page

Bookmarks

NCBIsub ; wPip ; Definitions ; Pop ; Perl ; C ; Linux

NCBI

• NCBI ; AA ; BLAST ; Microbial_Genomes ; SRA SRA_FTP ; TA ; TA_FTP ; Genomes_FTP ; Bacterial Genomes FTP ; Taxonomy CommonTree
• Complete Bacteria

Links

• Baylor
• EMBL
• EMBOSS
• Homo Sapiens Genome Projects
• JGI Microbial Genomes
• JGI Genomes Online (GOLD)
• JGI Integrated Microbial Genomes (IMG)
• Sanger
• Sanger Microbial Genomes
• CBCB
  • NCBI complete genomes: /fs/szdata//ncbi/genomes/Bacteria/ (*.fna)
  • Personal web site http://www.cbcb.umd.edu/~dpuiu -> /fs/www/users/dpuiu/
  • Personal ftp site ftp://ftp.cbcb.umd.edu/pub/data/dpuiu -> /fs/ftp-cbcb/pub/data/dpuiu/
• ARKDB genetic maps - cow, chicken ...

Projects

DHS genomes

• Bioterrorism
• Bacillus anthracis
• Burkholderia mallei
• Burkholderia pseudomallei
• Clostridium botulinum (Hall strain A str. ATCC 3502) ; uploaded to Insignia ; (other) ; some uploaded to Insignia
• Clostridium perfringens ; some uploaded to Insignia
• Cryptosporidium hominis (test)
• Francisella tularensis OSU18 in Insignia
• Francisella tularensis some uploaded to Insignia
• Salmonella (Washington Univ in St Louis)
• Yersinia enterocolitica
• Yersinia pestis

Other genomes

• Brugia malayi
• Bos taurus , Bos taurus redo , Bos taurus 3.0
• Coffee BACs
• Culex pipiens wolbachia symbiont
• Culex pipiens wolbachia mitochondrion
• Helicobacter pylori
• Homo sapiens
• Pseudomonas aeruginosa
• Pseudomonas syringae
• Sea urchin
• Turkey
• Xanthomonas oryzae
• Strawberry

Other

• Sequencing
• Alignment *
• CA ; Assembly
• Comparative assemblies
• Metagenomics
• NCBI submission
• Repeat search
• Vector trimming
• Data formats

• Definitions
• Meeting notes
• My articles
• CS ; Perl ; C ; Linux ; DOS ; wiki
• Pop group meeting (Monday 's 3pm)

• ToDo

Test data sets

Sanger

• 23,536 reads
• 11,652 mates
• 1 lib : 4.5K mean
• Location

 /fs/szasmg/Bacteria/F_tularensis/TA_FTP/libs/G878A1.frg 

Solexa unpaired

• 2,659,250 36bp reads
• Location:

 /fs/szdata/Solexa/Streptococcus_suis/suisp17/strip3.fna