Results for "blast"

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  • 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

    2300 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

    2207 days ago

  • NCBI Magic-BLAST

    Magic-BLAST is a tool for mapping large next-generation RNA or DNA sequencing runs against a whole genome or transcriptome. Each alignment optimizes a composite score, taking into account simultaneously the two reads of a pair, and in case of RNA-seq, locating the candidate introns and adding up ...

    Tags: NCBI, Magic-BLAST, Documentation, RNA-seq, Mapping, BLAST

    2053 days ago

  • BLAST nr version 5 database, (nr_v5)

    NCBI have made changes the nr version 5 database, (nr_v5), to facilitate better search results and improved performance by reducing the number of redundant titles in the nr_v5 database used by webBLAST, which is also available for BLAST+ users. The changes in nr preserve the taxonomic div...

    Tags: BLAST, NCBI, nr, version, 5, database, nr_v5

    1679 days ago

  • BLAST+ 2.10.0 released

    The BLAST+ 2.10.0 release is now available from at FTP site.  The new version offers the following improvements: updated composition-based statistics for protein-protein (including translated BLAST) comparisons to provide stable results when you request fewer than the default number ...

    Tags: BLAST+ 2.10.0, release, available, FTP, site, version, offers, improvements, BLAST, blast

    1562 days ago

  • New Layout for BLAST ftp Database Site

    As announced previously, the new default database version for BLAST+ is dbV5.  To complete this transition, the ftp database site will be updated to support this change.  We expect this change to happen around February 4th, please adjust your scripts or procedur...

    Tags: New, Layout, BLAST, ftp, Database, Site

    1528 days ago

  • Magic-BLAST

    Magic-BLAST is a tool for mapping large next-generation RNA or DNA sequencing runs against a whole genome or transcriptome. Each alignment optimizes a composite score, taking into account simultaneously the two reads of a pair, and in case of RNA-seq, locating the candidate introns and adding up ...

    Tags: NCBI, Magic, BLAST, Documentation

    1469 days ago

  • Primer BLAST !

    BLAST team added a new feature (Max 3' match), shown in Figure 1, to Primer-BLAST that limits the length of 3' exon matches when designing exon-exon spanning primers. This makes it less likely that primers specifically designed to amplify transcripts will also amplify genomic DNA contamination in...

    Tags: Primer, BLAST, Feature, Alignments !

    1431 days ago

  • BLAST+ 2.11.0 release is now available on FTP site !

    BLAST+ 2.11.0 release is now available from our FTP site. The main advance is the ability to provide usage reports to NCBI to help us improve BLAST. This information is limited to the name of the BLAST program, some basic database metadata, a few BLAST parameters, as well the number and total siz...

    Tags: BLAST, 2.11.0, release, available, FTP, site

    1230 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

    1213 days ago