User: shalinikaushik1293

Reputation:
0
Status:
New User
Last seen:
1 month, 1 week ago
Joined:
6 months, 2 weeks ago
Email:
s*****************@gmail.com

Profile information, website and location are not shown for new users.

This helps us discourage the inappropriate use of our site.

Posts by shalinikaushik1293

<prev • 22 results • page 2 of 3 • next >
0
votes
1
answer
198
views
1
answers
Comment: C: time taken by pgenthreader.sh script
... My query is : >NP_000160.1 alpha-galactosidase A precursor [Homo sapiens] MQLRNPELHLGCALALRFLALVSWDIPGARALDNGLARTPTMGWLHWERFMCNLDCQEEPDSCISEKLFM EMAELMVSEGWKDAGYEYLCIDDCWMAPQRDSEGRLQADPQRFPHGIRQLANYVHSKGLKLGIYADVGNK TCAGFPGSFGYYDIDAQTFADWGVDLLKFDGCYCDSLENLADGYKHMSLALNRTGRSIVYSCEW ...
written 6 months ago by shalinikaushik12930
0
votes
1
answer
198
views
1
answer
time taken by pgenthreader.sh script
... I am running the pgenthreader.sh script and runpsipred script and it took approx 3 to 4 hours to run the runpsipred script and approx 8 hours to run the pgenthreader.sh script for a single protein fasta file. Is this the usual time these scripts take to predict the fold and secondary structure of ...
pgenthreader psipred blastpgp written 6 months ago by shalinikaushik12930
0
votes
0
answers
343
views
0
answers
Comment: C: BLAST nr database
... Thank you @prince26121991 for the help. ...
written 6 months ago by shalinikaushik12930
0
votes
0
answers
343
views
0
answers
Comment: A: BLAST nr database
... That means I need to use an external disc for nr database because in future, results will also need space. As I am using BLAST for `~7000` proteins. Yes I am sure, there were no errors when I built the index. Can you please tell me in all the nr database files (you have sent me the link), which one ...
written 6 months ago by shalinikaushik12930
0
votes
0
answers
169
views
0
answers
Comment: A: psipred error. Unmatched '`'.
... I saw your previous message that I should use code instead of bold, after I posted this question. I am using this command from the pgenthreader.sh script. because that script is encounter with the error PSIPRED failed...exiting early. So, I tried to run the PSIPRED command separately on shell...so ...
written 6 months ago by shalinikaushik12930
0
votes
0
answers
343
views
0
answers
Comment: C: BLAST nr database
... It's 16 GB RAM memory in the macOS, I am using ...
written 6 months ago by shalinikaushik12930
0
votes
0
answers
343
views
0
answers
Comment: C: BLAST nr database
... Thank you for your reply and suggestion I will use code button from the next time. Yes, the command line is running with `=` sign also. I didn't use the pre-built indexes because I am not finding the complete nr database. It is divided into parts (like nr.00.tar.gz, nr.01.tar.gz, etc.). So, I found ...
written 6 months ago by shalinikaushik12930
0
votes
0
answers
169
views
0
answers
psipred error. Unmatched '`'.
... i ran a psipred command of pgenthreade.sh script **tcsh psipred /media/kakarot/ppi/genthreader/sequence.iter3.mtx /media/kakarot/ppi/psipred/data/weights.dat /media/kakarot/ppi/psipred/data/weights.dat2 /media/kakarot/ppi/psipred/data/weights.dat3 > /media/kakarot/ppi/genthreader/sequence.pgen.s ...
psipred tcsh shell linux written 6 months ago by shalinikaushik12930
0
votes
0
answers
343
views
0
answers
BLAST nr database
... I am running the command for BLAST : blastp -query /Users/shalini/Desktop/shalini/project/unmodelled_fasta/AAA18895.fasta -outfmt "7 sacc qcovs pident ppos evalue" -db=/Users/shalini/Downloads/nr -out=/Users/shalini/Desktop/shalini/project/blast_resultnr After running for one and half hour, it ...
nr database blast written 6 months ago by shalinikaushik12930
0
votes
1
answer
194
views
1
answers
Comment: A: issue with psipred
... Thank u so much for your reply. I have typed the correct path where the program is exist. I think the problem is with psipred. I have read the README file... it ask to use the tcsh shell to execute the psipred command. As I am using Linux (Ubuntu), It requires csh instead of tcsh. I installed and ch ...
written 6 months ago by shalinikaushik12930 • updated 6 months ago by genomax85k

Latest awards to shalinikaushik1293

No awards yet. Soon to come :-)

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1824 users visited in the last hour