User: Neha shri

gravatar for Neha shri
Neha shri30
Reputation:
30
Status:
New User
Location:
United States
Last seen:
3 years, 5 months ago
Joined:
3 years, 8 months ago
Email:
s******************@gmail.com

Posts by Neha shri

<prev • 30 results • page 1 of 3 • next >
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Can shuffling a certain percentage of amino acid residues within a protein, change the fold it adopts?
... Dear all,             I am working on a project concerning Inverse folding Problem. I have a protein of interest which apparently mis-folds , after  a certain age and cause aggregation.                                                The protein has 200 (approx) residues out of which 92 residues ar ...
threading sequence conserved inverse folding written 3.5 years ago by Neha shri30
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What is most likely to be used, Homology or ab-initio based method?
... Dear all,               Suppose if i have a database of protein sequences , and each sequence in it shares a sequence similarity of more than 50 % with a sequence for which crystal structure is already available in the PDB.                    Is it likely that any sequence in the database would fo ...
ab-initio sequence homology 3d-modelling written 3.5 years ago by Neha shri30 • updated 3.4 years ago by Biostar ♦♦ 20
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Can a locally created database be used instead of NR in I-TASSER?
... Dear all,                  I have generated a database of protein sequences and selected a few sequences from it based on some criteria. Now i would like to model these selected sequences and see if they folded into the native structure of a protein. The protein (native)  shares a sequence similari ...
software error 3d modelling blast written 3.5 years ago by Neha shri30
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Error message " library files are not complete" while running the ./runI-TASSER.pl script?
... Hello ,  I am new to protein modelling using I-tasser package. I have manually downloaded the I-tasser library files and decompressed them into a directory of I-tasser package. When i am running the runI-TASSER.pl script, The error says- Your library files are not complete, please download libra ...
perl i-tasser library written 3.5 years ago by Neha shri30 • updated 3.4 years ago by Biostar ♦♦ 20
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Comment: C: How to download a large file from a computer which is behind squid proxy?
... Hello Alex Reynolds! The files i was trying to download were I-Tasser library files for modelling a small protein database.  One might encounter the same error while downloading the protein databases from NCBI (Stand-alone Blast) or any database for that matter. Since all the computers in my locat ...
written 3.5 years ago by Neha shri30
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(Closed) How to download a large file from a computer which is behind squid proxy?
... Hi ,      I am unable to download a few files which are 958 and 560 mb of size respectively .                     The error says:                 The request or reply is too large.                    If you are making a POST or PUT request, then the item you are trying to upload is too large.   ...
squid proxy written 3.5 years ago by Neha shri30
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Comment: C: Is there any format specifier in BLAST+ which enables to get full length of fas
...  Thank you so much :) exactly what i was looking for. ...
written 3.6 years ago by Neha shri30
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Is there any format specifier in BLAST+ which enables to get full length of fasta sequences (subject) in the output along with other specifiers?
... Hi,             I am using blast+ and have a database of thousands of protein sequences. Could you please tell me how to get the entire length of every sequence in the output file along with other specifiers .I tried with sseqid but it gives out only the ids not the entire sequence. ...
alignment sequence blast written 3.6 years ago by Neha shri30 • updated 3.6 years ago by Jenez520
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Comment: C: How to get the maximum number of hits in BLAST 2.2.31+?
... Thank you so much :) I am able to do it now. Could you please also tell me a way to get the full fasta sequences in the output instead of only their sequence ids?     ...
written 3.6 years ago by Neha shri30
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How to get the maximum number of hits in BLAST 2.2.31+?
... Hi ,                 I have a locally created database which contains thousands of protein sequences . I want to check the positive substitutions in every sequence with reference to the target protein  as random substitutions were made in every sequence. The format specifier i am using is "positive ...
alignment blast written 3.6 years ago by Neha shri30 • updated 3.6 years ago by Protostome50

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