Tool:Clustering of short peptide sequences

Question

[jockbanan]

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

[xiaoyuzhangh]

Hi, I'm doing drug discovery research and I found Hammock. However when I run it. I got message like this:

Hammock version 1.1.4 Run with --help for a brief description of command line parameters.

HHLIB env. variable not set. Setting to: /Users/xiaoyuzhang/Hammock_v_1.1.4/hhsuite-2.0.16/lib/hh/ Error. Run with --help for a brief description of command line parameters. Trace:

java.io.IOException: Error, Clustal Omega won't run properly. Make sure it runs and try again. original error message: [/Users/xiaoyuzhang/Hammock_v_1.1.4/clustal-omega-1.2.0/clustalO-64bit stderr]: /Users/xiaoyuzhang/Hammock_v_1.1.4/clustal-omega-1.2.0/clustalO-64bit: /Users/xiaoyuzhang/Hammock_v_1.1.4/clustal-omega-1.2.0/clustalO-64bit: cannot execute binary file original stdout message:

at cz.krejciadam.hammock.Hammock.checkExternalProgram(Hammock.java:1413)
at cz.krejciadam.hammock.Hammock.checkClusteringArgs(Hammock.java:1305)
at cz.krejciadam.hammock.Hammock.parseArgs(Hammock.java:259)
at cz.krejciadam.hammock.Hammock.main(Hammock.java:142)

Could you give me some help to solve the problem? Many thanks!

[jockbanan]

Hi! Thanks for your interest in Hammock. The best place to talk about technical problems of the tool is the Github issues page:

https://github.com/krejciadam/hammock/issues

According to the error message, it seems Clustal Omega does not run properly on your machine. Can you run the Clustal executable?:

/Users/xiaoyuzhang/Hammock_v_1.1.4/clustal-omega-1.2.0/clustalO-64bit

Make sure the file has executable permissions. If it does and still won't, you might need to compile Clustal Omega on your machine.

If this does not help, feel free to ask the question in the Github Issues page, we can discuss it there.

[xiaoyuzhangh]

Thanks a lot! I can't run the Clustal Omega.

[nbp-25-183-57:~] xiaoyuzhang% /Users/xiaoyuzhang/Hammock_v_1.2.0/clustal-omega-1.2.0/clustalO-64bit ; exit; /Users/xiaoyuzhang/Hammock_v_1.2.0/clustal-omega-1.2.0/clustalO-64bit: Exec format error. Binary file not executable. logout

I will move to Github