Tag: .faa
gff3 – Extracting animo acid and nucleotide sequences from KofamScan output and codon alignment
I want to extract the amino acid sequences from KofamScan output, and my workflow is as attached in the picture: For the analysis I am doing, I need to get the animo acid sequences, align them, and do codon alignment with the corresponding nucleotide sequences, so that I can get…
Mac program for DNA analysis and cloning.
Tool:BioLabDNA – Mac program for DNA analysis and cloning. 0 BioLabDNA is one time purchase program with lifetime updates including new features. This program is aimed at researches in the molecular biology field. BioLabDNA is the document based app focused on the analysis and manipulation of DNA sequences. The user…
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…
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 ?…
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…
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…
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….
