Tool: Clustering of short peptide sequences
4
gravatar for jockbanan
3.5 years ago by
jockbanan370
Czech Republic
jockbanan370 wrote:

Dear Biostars community, 

We would like to introduce new software for peptide sequence clustering. Simply, it takes input peptide sequences, identifies clusters of peptides sharing sequence motifs, and generates multiple sequence alignments of resulting clusters. So if you have something like this: 

YRPLPTVPRYIE
SRYLSSVPERNY
YLFRALPDVPRN
WYHGLPAVPMYN
YAPMLPTRYVGE
WVVRPLPVVGAF
GPLLPVRSADLL
YMPALPSRNWGP
VPPVPARSHGVF
SYVPGVPLRNLA
YRALPVFPTMSE
WRSLPVIPTYEF

You'll get this: 

--YRPLPTVPRYIE
--YRALPVFPTMSE
YLFRALPDVPRN--
-WYHGLPAVPMYN-
WVVRPLPVVGAF--
--WRSLPVIPTYEF

And this: 

---GPLLPVRSADLL
--YMPALPSRNWGP-
--YAPMLPTRYVGE-
---VPPVPARSHGVF
-SYVPGVPLRNLA--
SRYLSSVPERNY---

 

The software is primarily meant to process data resulting from combinatorial peptide library experiments (such as phage display) sequenced using NGS, but no limits are put on the origin of data. It can process up to millions of unique peptide sequences. 

 

Links: 

software + manual + source code: 

https://github.com/hammock-dev/hammock/releases

Galaxy version: 

https://toolshed.g2.bx.psu.edu/view/hammock/hammock/afddbcbc8ee8

Publication: 

http://www.ncbi.nlm.nih.gov/pubmed/26342231

 

 

ADD COMMENTlink modified 6 days ago • written 3.5 years ago by jockbanan370
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