Results for "blastn"
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I am doing megablast of a contig against NR database, but unable to understand this -outfmt '6 qseqid staxids qstart qend sstart send qseq sseq evalue length' Can you please help me to undestand all these.Tags: Blastn, BLAST, Nucleotide, Alignment, Database, NR, Contig, NGS
2868 days ago
RepeatMasker compatible blast tool
RMBlast is a RepeatMasker compatible version of the standard NCBI blastn program. The primary difference between this distribution and the NCBI distribution is the addition of a new program "rmblastn" for use with RepeatMasker and RepeatModeler. RMBlast supports RepeatMasker searches by adding a...Tags: RMBlast, Repeat, Maskers, Blastn, blast, Download
1968 days ago
How to print only the first best hit from blastn tool?
I used the following command to print the blast hit. [Terminal] blastn -query aaa.fa -db blastdb/nt -evalue 10e-5 -num_threads 4 -max_target_seqs 1 -outfmt '6 qseqid staxid qstart qend sallseqi sstart send evalue length frames qcovs' -out testBlastSee But the outfile print many hits, I only...Tags: blastn, blastall, megablast, top, hits
2612 days ago
Converting BLAST output into CSV
Suppose we wanted to do something with all this BLAST output. Generally, that’s the case - you want to retrieve all matches, or do a reciprocal BLAST, or something. As with most programs that run on UNIX, the text output is in some specific format. If the program is popular enough, there w...Tags: Convert, BLAST, output, CSV, blastn, megablast
2329 days ago
Basic command-line to run BLAST
The goal of this tutorial is to run you through a demonstration of the command line, which you may not have seen or used much before. All of the commands below can copy/pasted. Install software Copy and paste the following commands sudo apt-get update && sudo apt-get -y ...Tags: Basic, command-line, run, BLAST, blastn, blastp
2236 days ago
Understanding BLASTn output format 6 !
BLASTn output format 6 BLASTn maps DNA against DNA, for example gene sequences against a reference genomeblastn -query genes.ffn -subject genome.fna -outfmt 6 BLASTn tabular output format 6 Column headers:qseqid sseqid pident length mismatch gapopen qstart qend sstart send eva...Tags: BLASTn, blast, alignment, output, format, 6
2130 days ago
