User: shalinikaushik1293

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Posts by shalinikaushik1293

<prev • 22 results • page 1 of 3 • next >
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automation of shell script where I want to change filename after every result
... Hello everyone I want to run the pGenThreader script for a 7,000 proteins but for that I need to replace the protein file after every result of previous protein. I need to automate the script. If anyone can help me with this. The pGenThreader script is #JOB name JOB=testing #input ...
automation shell written 5 weeks ago by shalinikaushik12930
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missing .chk and .mtx files after using psipred script.
... Hello, I am running my python program on two systems. 1. Ubuntu 18.04.4 LTS (62.6 GiB, 64 bit) 2. CentOS kernel Linux 2.6.32-504.16.2.el6.x86_64 GNOME2.28.2 I am running the python code given below: import os import shutil from multiprocessing import Pool as ThreadPool import mul ...
.mtx .chk psipred linux written 7 weeks ago by shalinikaushik12930
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Promals is not taking the accurate name of FASTA sequence
... I am trying to use promals on the multiple sequences which are placed in a file. The file (NP_689570-negative.fasta) contains : >UniRef100_A0A0D9R2V9 Uncharacterized protein n=1 Tax=Chlorocebus sabaeus TaxID=60711 RepID=A0A0D9R2V9_CHLSB MFQDSVVFEDVAVNFTQEEWALLGPSQKKLYRDVMQETFVNLASIGENWEEKN ...
fasta promals written 3 months ago by shalinikaushik12930
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experimentally validated protein protein interactions
... Hello everyone, Can anyone tell me from where I can get the experimentally validated results of protein protein interaction between human and different pathogens. Please share the information regarding this. I really need the help. I will be thankful. Looking forward for the replies. ...
human proteins ppi invitro written 4 months ago by shalinikaushik12930
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Comment: C: wrong version of formatdb was used to make database
... I am using macOS High Sierra, processor is 3.3 GHz Intel Core i7 and the memory is 16 GB 1867 MHz DDR3. Looking forward for your reply. I need your help. ...
written 4 months ago by shalinikaushik12930
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Comment: C: wrong version of formatdb was used to make database
... Thank you so much for your reply. I resolved the problem by using formatdb. But after running the program for 3 hours for a single protein. It gives me the error: Running PSI-BLAST with sequence /Users/shalini/Desktop/pgen_github/unmodelled_fasta/AAA18895.fasta ... [blastpgp 2.2.26] WARN ...
written 4 months ago by shalinikaushik12930
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wrong version of formatdb was used to make database
... I am using uniref100 database for running the psipred script (runpsipred) on macOS. On running the runpsipred script : #!/bin/tcsh # This is a simple script which will carry out all of the basic steps # required to make a PSIPRED prediction. Note that it assumes that the # fol ...
blastpgp runpsipred formatdb written 4 months ago by shalinikaushik12930 • updated 4 months ago by Mensur Dlakic5.4k
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Comment: C: time taken by pgenthreader.sh script
... Sorry, the hard drive is internally mounted. I am trying to use GNU parallel. Thank you so much for your help. I also tried to install `GPU-BLAST` (to speed up the BLASTp), but on running it's `install` script as `sh install` The error is: install: 6: install: function: not found -ne . ...
written 4 months ago by shalinikaushik12930
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using pfilt on uniref100 database
... Is it necessary to use `pfilt` on `uniref100` database before we use `BLAST` on the query? The information related to pfilt is there in the given link: http://bioinfadmin.cs.ucl.ac.uk/downloads/pfilt/ Anyone please suggest. ...
uniref100 pfilt blastp written 4 months ago by shalinikaushik12930
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Answer: A: time taken by pgenthreader.sh script
... Is it necessary to use `pfilt` on `uniref100` database before we use `BLAST` on the query? The information related to pfilt is there in the given link: http://bioinfadmin.cs.ucl.ac.uk/downloads/pfilt/ Anyone please suggest. ...
written 4 months ago by shalinikaushik12930

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