Tag: Makeblastdb

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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Blast database built error

Blast database built error 1 makeblastdb -in nt -dbtype nucl -out nt Building a new DB, current time: 12/09/2021 15:55:27 New DB name: /home/internal/Databases/NT/NT_Jul2021/nt New DB title: nt Sequence type: Nucleotide Deleted existing Nucleotide BLAST database named /home/internal/Databases/NT/NT_Jul2021/nt Keep MBits: T Maximum file size: 1000000000B No volumes were created. Error:…

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BLAST multiple sequences against each other from one FASTA file

BLAST multiple sequences against each other from one FASTA file 1 Hi, I am a beginner to using BLAST locally on Mac OSX. I have downloaded ncbi-blast-2.2.31+.dmg and have installed it. I have a FASTA file with multiple protein sequences in it and am trying to BLAST each sequence against…

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create protein database for local Blast

create protein database for local Blast 1 Hello friends, how’re you? I wanted to know how I can do a blast against a database that I downloaded. I’ve downloaded a database of protein sequences from DEG (essential genes) and my idea is to do a blast against this database in…

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Create de novo repeat library

Tutorial for de-novo repeat library construction The RepeatMasker software includes a lot repeat library. You can query them using: queryTaxonomyDatabase.pl -h queryRepeatDatabase.pl -h If there is no repeat library available for your species, you may want to create your own.Prerequisite Lot of time (the repeatmodeler and transposonPSI steps can run…

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makeblastdb Bus error

makeblastdb Bus error 0 problem: $makeblastdb -in $reference -parse_seqids -title “hg19” -dbtype nucl Building a new DB, current time: 08/16/2021 14:21:54 New DB name: New DB title: hg19 Sequence type: Nucleotide Deleted existing Nucleotide BLAST database named Keep MBits: T Maximum file size: 1000000000B Bus error version: $makeblastdb -version makeblastdb:…

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Use BLAST Command Line Applications to run a folder of many sequences against a database

Use BLAST Command Line Applications to run a folder of many sequences against a database 0 Hi everyone, I am quite new to using the BLAST Command Line Applications and would love any and all help. I am trying to use the application to run many sequences stored in a…

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blastx versus tblastx

hello everyone I have a question about the blast. I admit that I do not understand everything. I have been asked to blastx an fsa file of arabidopsis thaliana sequences against an oak gene model. In order to see if there were any matching sequences between the two species: My…

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