Tag: .faa

makeblastdb creating multiple files of unexpectedly large sizes

I have a set of 100 amino acid sequences and I want to perform a BLASTP sesrch against the refseq_protein database. Accordingly I had set up the standalone version of BLAST (Version 2.11.0+) and downloaded the refseq_protein database from NCBI using the following code wget ftp.ncbi.nlm.nih.gov/refseq/release/complete/*.faa.gz The database gets downloaded…

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How to taxonomically subsample a proteomes file ?

How to taxonomically subsample a proteomes file ? 0 I have a proteomes .faa file with all the protein sequences encoded by LUCA. I want to create a file with the proteomes of only a few specific eukaryotes, few specific archaea and all bacteria. How do I do this ?…

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New Mac program for molecular biologists

Tool:New Mac program for molecular biologists 12 I would like to present here a program – BioLabDonkey – for molecular biologists who are Mac users. This program is written from scratch in a language native for Mac – Swift. The program can be downloaded from mac App Store – apps.apple.com/us/app/biolabdonkey/id1470827582?ls=1&mt=12…

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How to split big .faa file into smaller .faa files

How to split big .faa file into smaller .faa files 1 I have a 10 gb .faa proteomes file that I want to run MAFFT on. But it is too big and hence I need to divide the file. How do I convert it to smaller files in windows without…

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Help speeding up HMMER’s HMMSearch algorithm for large fasta file with GNU Parallel

I’ve seen that HMMER can be sped up with GNU Parallel: Speed of hmmsearch I have around 100,000 sequences and a HMMER database of around 300 HMM profiles. I’m running everything at once but I’m wondering if it’ll be faster to split up the sequences and/or split up the jobs….

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