User: mnsp088

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mnsp08820
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Posts by mnsp088

<prev • 6 results • page 1 of 1 • next >
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Comment: C: Fast way to extract specific sequences from large fasta
... Thank you for your suggestions, and all suggestions below. I would like to report that I have run all of them, and your solution > samtools faidx -r $file master_fasta.fs > ./fastas/$file2.fa was the quickest. faSomeRecords also sped it up a lot, but this solution was still quicker. Thanks ...
written 2 days ago by mnsp08820
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Fast way to extract specific sequences from large fasta
... Hi all! I have ~2k text files, each with ~1k protein names (one protein name per line) and I need to extract the sequences of these proteins from a large master fasta file which contains ~5.5 million sequences. I wrote this code to do this task and it works but it is taking a really long time to pr ...
fasta sequencing written 3 days ago by mnsp08820 • updated 2 days ago by jrj.healey12k
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Comment: C: HH-suite custom db with precomputed MSA
... I thought ffindex_from_fasta creates the files to be used to make the MSA using hhblits and their uniclust db: > hhblits_mpi -i _fas -d -oa3m _a3m_wo_ss > -n 2 -cpu 1 -v 0 but since I already have a precomputed MSA I skipped these steps and tried to build the HMM profile directly. Is this p ...
written 8 days ago by mnsp08820
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HH-suite custom db with precomputed MSA
... Hi everyone. I am trying to create a custom database in HH-suite using a precomputed multiple sequence alignment (MSA) that I got from MUSCLE. I'm following the steps outlined here: [https://github.com/soedinglab/hh-suite/wiki#building-customized-databases][1] and I skipped to making the HMM model s ...
hh-suite hmm msa written 8 days ago by mnsp08820
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Comment: C: Tools for functional annotation of proteins
... I am trying it out right now, thank you for the suggestion! ...
written 10 days ago by mnsp08820
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Tools for functional annotation of proteins
... Hello, Does anyone know of a tool for functional annotation of protein sequences with input being amino acid sequences in fasta format and with the ability to download it and run it via command line? I know BlastKoala does functional annotation of sequences but users must submit to their web server ...
annotation proteins blastkoala written 10 days ago by mnsp08820

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