Fwd: [MSI #67787] AutoReply: addition of features in Galaxy-P (proteases)

[Ebbing de Jong]

Hi, Pratik asked me to forward this message to the Galaxy-P distribution
list.

Good afternoon,

I would like to request that two tools in Galaxy-P be expanded. These
are found at:

- Proteomics: Community -> FASTA Manipulation -> ProteinDigestor
(version 2.0)
- Proteomics: Community -> FASTA Manipulation -> Digest Database
(version 0.1.0)

Each of these tools allows the user to select an enzyme or protease, but
the list of available enzymes is far from complete. I recommend that all
the available enzymes from the ProteinPilot tool (there called
Digestion) be implemented into the aforementioned tools. For a more
exhaustive list, or for digestion rules, please see here
(http://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html).
Specifically, I would like to see the inclusion of Arg-C, Glutamyl
endopeptidase (aka Glu-C), proline-endopeptidase and pepsin.

Similarly, the X!Tandem MSMS Search tool could benefit from the same
(expanded) list of proteases.

Cheers,
Ebbing

[Björn Grüning]

Hi,

Pratik where is the source of these repositories stored?

Ciao,
Bjoern

[Lennart Martens]

Hi,


Sorry to barge into this out of the blue, but the topic prompted me to
suggest that perhaps we could consider adding our DBToolkit
(https://code.google.com/p/dbtoolkit/) at some point.

It knows how to do nearly any trick to a database, and (like SearchGUI
and PeptideShaker) runs in command line mode as well as GUI mode. It's
also a long-standing piece of software (ten years old :)) that has
become very feature-rich and rock-solid stable over the years.

Some features of DBToolkit:

- Digestion, including a full predefined enzyme list + custom
definable enzymes (including regular expression-based enzymes)
+'bifunctional enzymes' (creates peptides where the N-temrinus is
cleaved according to a different enzyme specificity than the C-terminus;
great for studying in vivo protease cleavage followed by trypsin)

- Replacing residues in sequences based on regular expressions

- Filtering of entries based on their location, weight, or composition
(custom format [e.g. ">2R AND (L OR I) AND !W"] or regular expression)

- 'ragging' of databases

- Creating shuffled or reversed versions

- Lossless removal of sequence-level redundancy

- Ability to 'mature' sequences from UniProtKB/Swiss-Prot (i.e.,
removing all annotated pre- and pro-peptides)

- Sensible parsing of very many different types of FASTA headers


Should you be interested, the manual tells you everything :).

https://code.google.com/p/dbtoolkit/source/browse/trunk/src/main/resources/about.txt


Cheers,

lnnrt.

[Ira Cooke]

Hi Ebbing,

Thanks for your email. I maintain the X!Tandem tool, and will take a look at your link to incorporate the available enzymes.

Cheers
Ira

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[Pratik Jagtap]

Hello Bjoern,

We are requesting one of our MSI developers to make changes and install the software. We will let you know where the refurbished software would be available.

Thanks,

Pratik

Pratik Jagtap,

Managing Director,

Center for Mass Spectrometry and Proteomics,

43 Gortner Laboratory
1479 Gortner Avenue
St. Paul, MN 55108

Phone: 612-624-9275