User: ddofer

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ddofer30
Reputation:
30
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New User
Location:
Israel
Last seen:
1 year, 6 months ago
Joined:
5 years, 11 months ago
Email:
d*****@gmail.com

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Posts by ddofer

<prev • 10 results • page 1 of 1 • next >
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Get a CSI-BLAST PSSM
... I'm trying to get the PSSMs (i.e per=site probability of each AA) for a batch of protein sequences.  I haven't used PSI-BLAST or CS-BLAST in the past, and am unfamiliar with the exact commands needed to pipe them together, and to get the output. I'd like to use CSI-BLAST on each sequence, then to ...
pssm cs-blast protein psi-blast written 4.8 years ago by ddofer30
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Getting BLAST Clusters Classifier performance for Protein classes
... I have a number of protein datasets, that I applied my machine learning method (ProFET) to, for classification (i.e. using machine learning).  The reviewers want a comparison of our methods performance, vs PSI-BLAST.  I have various sets of protein sequences, each in its own multi-fasta file, with e ...
sequence proteins blast machine learning written 4.9 years ago by ddofer30 • updated 4.8 years ago by mark.ziemann1.2k
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Comment: C: Removing Sequences With More Than 90% Identity In A Protein Fasta File
... t_coffee's option removes one of a pair, not both. ...
written 4.9 years ago by ddofer30
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Comment: C: Constructing A Multiple Sequence Alignment With An Extended Alphabet
... I'm looking at the exact same thing! (Did you ever find a solution? Thanks!) ...
written 5.1 years ago by ddofer30
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Q: Extracting dibasic PC Cleavage sites
... I want to get a dataset of all known, validated cleavage sites, of prepro-hormone/protein precursors (e.g. insulin, neuropeptide precursors..) , cleaved by PCs (e.g. Furin..).  I'm looking for only annotated or verified sites, so I can't just extract a window from any sequence containing a [KR][KR] ...
ptm cleavage sequence uniprot furin written 5.2 years ago by ddofer30 • updated 5.1 years ago by Elisabeth Gasteiger1.7k
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Answer: A: How Can I Count Dipeptide (Or Features Of Protein Sequences) In Multiple Protein
... I'm actually in the final stages of a comprehensive package for doing exactly this right now!  That said, here's an older prototype, that should do all the things you're looking for (dipeptides, etc' ).   http://www.protonet.cs.huji.ac.il/neuropid/code/index.php   NPID_WebPackage.zip (You ...
written 5.6 years ago by ddofer30
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Comment: C: Finding Proteins that have NO known Domains
... Interpro has many annotations though, not just domains... (And I'm wokring on offline sequences which aren't necessarily in Uniprot; or even NCBI. As for your approach on a database, Wouldn't i make more sense to just search for proteins with "NOT domain:*" ?  Your query has proteins with annotate ...
written 5.6 years ago by ddofer30
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Comment: C: Finding Proteins that have NO known Domains
... I was working then with the HMMER and/or PFAM search results, which are returned as a plaintext email. Yuch.  That said, even with the offline tool, I don't know how to parse the command line output text properly, it just prints it onscreen. .  ...
written 5.6 years ago by ddofer30
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Answer: A: Database Of Structurally Derived Protein Features
... I wrote a feature generation program/script a while ago in python that can do a lot of this, it's very fast and local, so just run it against the fastas of the proteins you want.  (I'm currently working on a much upgraded version). Here's the source code.  http://www.protonet.cs.huji.ac.il/neurop ...
written 5.6 years ago by ddofer30
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Finding Proteins that have NO known Domains
... I want to extract a list of proteins for a given organism that have no (high confidence) predicted domains by PFAM or the like.  (Alternatively, getting a list of predictions for a list of proteins would also be good).    I know HMMER and Pfam and the like (CCD-Hit) have various tools for searchi ...
domain pfam sequence protein batch written 5.7 years ago by ddofer30 • updated 5.7 years ago by Elisabeth Gasteiger1.7k

Latest awards to ddofer

Popular Question 4.6 years ago, created a question with more than 1,000 views. For Finding Proteins that have NO known Domains
Supporter 4.9 years ago, voted at least 25 times.

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