Dpuiu alignment - Revision history

Dpuiu: /* Pairwise Alignment Processing (poster) */

2009-10-05T18:57:43Z

Pairwise Alignment Processing (poster)

← Older revision		Revision as of 18:57, 5 October 2009
Line 35:		Line 35:
	== Abstract==		== Abstract==

	* We present a software tool for ~~context based~~ sequence alignment processing.		* We present a software tool for sequence alignment processing.
			* The tool filters and clusters local alignments
	* The tool was initially developed for finding syntenic regions in large eukariotic genomes but could also be used for analyzing rearrangements in microbial genomes.		* The tool was initially developed for finding syntenic regions in large eukariotic genomes but could also be used for analyzing rearrangements in microbial genomes.
	* The ~~sofware~~ takes as input alignment data which is generally very fragmented (low identity) and noisy (repeats, rearrangements) and tries to filter and cluster it in		* The software takes as input alignment data which is generally very fragmented (low identity) and noisy (repeats, rearrangements) and tries to filter and cluster it in

	* A moving window approach is used for comparing each alignment to its neighbors and decide if it agrees or not with its neighbors. The alignments which clearly disagree get discarded.		* A moving window approach is used for comparing each alignment to its neighbors and decide if it agrees or not with its neighbors. The alignments which clearly disagree get discarded.
Line 45:		Line 46:
	== Motivation ==		== Motivation ==

	Sequence alignment is one of the ~~oldest~~ bioinformatics problems.		Sequence alignment is one of the most common bioinformatics problems.
	Due to its complexity there is no one general solution and multiple algorithms have been implemented for aligning different data set types. There is always a tradeoff between speed and accuracy.		Due to its complexity there is no one general solution and multiple algorithms have been implemented for aligning different data set types. There is always a tradeoff between speed and accuracy.

Dpuiu: /* Pairwise Alignment Processing (poster) */

2009-10-02T20:45:37Z

Pairwise Alignment Processing (poster)

← Older revision		Revision as of 20:45, 2 October 2009
Line 35:		Line 35:
	== Abstract==		== Abstract==

	We present a software tool for context based sequence alignment processing.		* We present a software tool for context based sequence alignment processing.
	The tool was initially developed for finding syntenic regions ~~between~~ large eukariotic genomes but could be ~~also~~ used for analyzing rearrangements in microbial genomes.		* The tool was initially developed for finding syntenic regions in large eukariotic genomes but could also be used for analyzing rearrangements in microbial genomes.
	The sofware takes as input alignment ~~output generated by di~~		* The sofware takes as input alignment data which is generally very fragmented (low identity) and noisy (repeats, rearrangements) and tries to filter and cluster it in

			* A moving window approach is used for comparing each alignment to its neighbors and decide if it agrees or not with its neighbors. The alignments which clearly disagree get discarded.
			* The process is run iteratively on increasingly larger window sizes till

Dpuiu at 17:07, 2 October 2009

2009-10-02T17:07:57Z

← Older revision		Revision as of 17:07, 2 October 2009
Line 24:		Line 24:
	528 PA14-PA7.filter.anc		528 PA14-PA7.filter.anc
	9 PA14-PA7.merge.anc		9 PA14-PA7.merge.anc


			----

			= Pairwise Alignment Processing (poster) =

			Daniela Puiu*, Arthur Delcher, Steven Salzberg
			University of Maryland, College Park

			== Abstract==

			We present a software tool for context based sequence alignment processing.
			The tool was initially developed for finding syntenic regions between large eukariotic genomes but could be also used for analyzing rearrangements in microbial genomes.
			The sofware takes as input alignment output generated by di


			== Motivation ==

			Sequence alignment is one of the oldest bioinformatics problems.
			Due to its complexity there is no one general solution and multiple algorithms have been implemented for aligning different data set types. There is always a tradeoff between speed and accuracy.



			== Objectives ==

			== Materials and Methods ==

			== Results ==

			== References ==

			== Acknowledgments ==

Dpuiu at 16:06, 30 September 2009

2009-09-30T16:06:08Z

← Older revision		Revision as of 16:06, 30 September 2009
Line 2:		Line 2:

	Programs:		Programs:
	* filter-anc.pl -max -percent -w -W		* filter-anc.pl -max -percent -w -W
	max: max distance between the ref_intercept (default 1,000,000)		max: max distance between the ref_intercept (default 1,000,000)
	percent: min percent agreement for keeping an alignment (default 25)		percent: min percent agreement for keeping an alignment (default 25)
	w: min window size (default 4)		w: min window size (default 4) => 1+w*2
	W: max window size (default 100)		W: max window size (default 100) => 1+W*2

			Bacterial genomes (few Mbp) use -max 100000 -W 10
			Mammalian genomes (few Gbp) use -max 1000000 -W 100

	* merge-anc.pl -max		* merge-anc.pl -max
	max: max distance between the ref_intercept (default 1,000,000)		max: max distance between the ref_intercept (default 1,000,000)

Dpuiu at 16:04, 30 September 2009

2009-09-30T16:04:17Z

← Older revision		Revision as of 16:04, 30 September 2009
Line 4:		Line 4:
	* filter-anc.pl -max -percent -w -W		* filter-anc.pl -max -percent -w -W
	max: max distance between the ref_intercept (default 1,000,000)		max: max distance between the ref_intercept (default 1,000,000)
	percent: min ~~pc of disagreements~~ for ~~deleting~~ an alignment (default 25)		percent: min percent agreement for keeping an alignment (default 25)
	w: min window size (default 4)		w: min window size (default 4)
	W: max window size (default 100)		W: max window size (default 100)

Dpuiu at 16:01, 30 September 2009

2009-09-30T16:01:59Z

← Older revision		Revision as of 16:01, 30 September 2009
Line 2:		Line 2:

	Programs:		Programs:
	* filter-anc.pl -max ~~<i>~~ -percent ~~<i>~~ -w ~~<i>~~ -W ~~<i>~~		* filter-anc.pl -max -percent -w -W
	max: max distance between the ref_intercept (default 1,000,000)		max: max distance between the ref_intercept (default 1,000,000)
	percent: min pc of disagreements for deleting an alignment (default 25)		percent: min pc of disagreements for deleting an alignment (default 25)
Line 8:		Line 8:
	W: max window size (default 100)		W: max window size (default 100)

	* merge-anc.pl -max ~~<i>~~		* merge-anc.pl -max
	max: max distance between the ref_intercept (default 1,000,000)		max: max distance between the ref_intercept (default 1,000,000)

Dpuiu at 16:01, 30 September 2009

2009-09-30T16:01:28Z

New page

= Filtering =

Programs:
* filter-anc.pl -max -percent -w -W 
max: max distance between the ref_intercept (default 1,000,000)
percent: min pc of disagreements for deleting an alignment (default 25)
w: min window size (default 4)
W: max window size (default 100)

* merge-anc.pl -max 
max: max distance between the ref_intercept (default 1,000,000)

* Example:
cat PA14-PA7.delta | ~/bin/shrinkIds.pl | ~/bin/DELTA/delta2anc.pl > PA14-PA7.anc
cat PA14-PA7.anc | ~/bin/DELTA/filter-anc.pl -max 100000 -W 10 > PA14-PA7.filter.anc
PA14-PA7.filter.anc | ~/bin/DELTA/merge-anc.pl -max 100000 > PA14-PA7.merge.anc
cat PA14-PA7.merge.anc | ~/bin/DELTA/anc2delta.pl > PA14-PA7.merge.delta

wc -l *anc
691 PA14-PA7.anc
528 PA14-PA7.filter.anc
9 PA14-PA7.merge.anc