[EMBOSS] stretcher issues
ricepeterm at yahoo.co.uk
Wed Feb 6 08:19:57 UTC 2019
Can you send me example sequences for these cases and I will take a look.
All the best,
On 05/02/2019 22:58, David Mathog wrote:
> EMBOSS 6.6.0 on Centos 6.9.
> Trying to align a bunch of 2-20kbp contigs against a 175kbp BAC with
> stretcher and some odd things are falling out. I think these point to a
> problem in the handling of end gaps in that program. It is invoked like
> stretcher -aseq BAC.fasta -bseq contig.fasta \
> -outfile pairs.fasta -aformat3 fasta -auto
> 1. If a ~25kbp contig aligns so that its final 12kb overlaps (nearly
> exactly, like 99.9% identity) with the first 12kbp of the BAC it the
> alignment produced is a total mess. It seems like stretcher cannot
> handle end gaps in this context at all, forcing the 12kbp which should
> be dangling unpaired off the left end of the BAC into alignment
> internally. needle doesn't work in this situation either since both of
> these commands segfault (on a nearly idle machine with 512Gb of RAM):
> needle BAC.fasta contig.fasta -outfile pairs.fasta -aformat3 fasta
> needle BAC.fasta contig.fasta -outfile pairs.fasta -aformat3 fasta \
> -endweight T -endextend 0 -endopen 1 -auto
> The ssw_test program from SSWlib handles this correctly. (Unfortunately
> it does a local alignment and so cannot replace needle in this context.)
> 2. This happens a lot:
> AATTC(lots of sequence)ATGAC... (BAC)
> A--------(...)----------TGAC... (contig)
> It will also shift two A's, but not 3, or shift AAT, and so forth.
> Needle doesn't do this when it runs the same alignment (with the 2nd
> command from the pair above).
> Needle is also much slower than stretcher.
> The contigs have been flipped if necessary so that they are all in the
> same direction
> as the BAC.
> David Mathog
> mathog at caltech.edu
> Manager, Sequence Analysis Facility, Biology Division, Caltech
> EMBOSS mailing list
> EMBOSS at mailman.open-bio.org
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