Dpuiu alignment

Filtering

Programs:

• filter-anc.pl -max -percent -w -W

 max:      max distance between the ref_intercept (default 1,000,000)
 percent:  min percent agreement for keeping an alignment (default 25)
 w:        min window size (default 4)   => 1+w*2
 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

 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

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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 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

• 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

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.