Results for "output"
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collinearity: scripts to parse and analyse MCScanX collinearity output
scripts to parse and analyse MCScanX collinearity outputTags: collinearity, scripts, parse, analyse, MCScanX, collinearity, output
2340 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
2328 days ago
“One code to find them all”: a perl tool to conveniently parse RepeatMasker output files
One code to find them all is a set of perl scripts to extract useful information from RepeatMasker about transposable elements, retrieve their sequences and get some quantitative information. Assemble RepeatMasker hits into complete TE copies, including LTR-retrotransposon Retrieve correspond...Tags: perl, tool, conveniently, parse, RepeatMasker, output, files
2153 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
gapFinisher: A reliable gap filling pipeline for SSPACE-LongRead scaffolder output
gapFinisher to process SSPACE-LongRead output to fill gaps after the scaffolding. gapFinisher is based on the controlled use of a previously published gap filling tool FGAP and works on all standard Linux/UNIX command lines. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6733440/Tags: gapFinisher, reliable, gap, filling, pipeline, SSPACE-LongRead, scaffolder, output
1443 days ago
NCBI BLAST have added new columns to the Descriptions
NCBI BLAST have added new columns to the Descriptions Table for web BLAST output. The new columns are Scientific Name, Common Name, Taxid, and Accession Length. Common Name and Accession Length are now part of the default display. You can click 'Select columns' or 'Manage columns' to add or...Tags: NCBI, BLAST, add, columns, Descriptions, Table, web, BLAST, output
1242 days ago
- The Pango nomenclature is being used by researchers and public health agencies worldwide to track the transmission and spread of SARS-CoV-2, including variants of concern. This website documents all current Pango lineages and their spread, as well as various software tools which can be used by re...
Tags: Pango, Lineage, Analysis, Output, Classification, SARS-CoV2
893 days ago
