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Forum: Bioinformatics 05-13-2016, 10:49 PM
Replies: 1
Views: 466
Posted By green tree
One option is to get the full alignments (instead...

One option is to get the full alignments (instead of tab-delimited format) and search for identical sub-alignments... doesn't sound very fun...
Forum: Bioinformatics 05-13-2016, 10:44 PM
Replies: 1
Views: 466
Posted By green tree
searching for short, nearly identical peptide matches between two genomes

I want to find all of the short, nearly identical peptide matches between two genomes. These matches are ~10bp in length, allowing for 1 or 2 mismatches, but no gaps.

When I do the BLAST search, I...
Forum: De novo discovery 02-20-2012, 03:19 PM
Replies: 5
Views: 1,425
Posted By green tree
Hi everyone, Thanks for the responses ! Zam,...

Hi everyone, Thanks for the responses ! Zam, great link and interesting paper ( I was actually just thinking about this in the human population)
Forum: De novo discovery 02-17-2012, 03:21 PM
Replies: 5
Views: 1,425
Posted By green tree
Finding *new* regions of DNA in genome assemblies

I am working on an experimental evolution project. We sequenced ~50 strains of bacteria that were isolated along a time course. I want to see if these strains acquired NEW genes during the...
Forum: De novo discovery 02-09-2012, 09:24 AM
Replies: 0
Views: 768
Posted By green tree
Finding differences in gene content with Illumina SRA?

I deleted this post because it was redundant (please delete it). Thanks!
Forum: Bioinformatics 06-26-2008, 05:20 PM
Replies: 236
Views: 510,814
Posted By green tree
Correct me if I am wrong, but I think that...

Correct me if I am wrong, but I think that ssahaSNP is more tuned for ABI *Sanger* reads and not ABI SOLiD reads. For shorter reads, you can use ssaha2 (it even has a preconfigured option for Solexa)...
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