<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/34600?offset=10 https://bioinformaticsonline.com/bookmarks/view/43985/visualise-blast-results Tue, 11 Oct 2022 03:15:10 -0500 https://bioinformaticsonline.com/bookmarks/view/43985/visualise-blast-results <![CDATA[Visualise blast results !]]> Kablammo helps you create interactive visualizations of BLAST results from your web browser. Find your most interesting alignments, list detailed parameters for each, and export a publication-ready vector image, all without installing any software.

 

Address of the bookmark: https://kablammo.wasmuthlab.org/

]]> Abhi https://bioinformaticsonline.com/bookmarks/view/38449/koala-keggs-internal-annotation-tool-for-k-number-assignment-of-kegg-genes-using-ssearch-computation Wed, 12 Dec 2018 09:16:55 -0600 https://bioinformaticsonline.com/bookmarks/view/38449/koala-keggs-internal-annotation-tool-for-k-number-assignment-of-kegg-genes-using-ssearch-computation <![CDATA[KOALA: KEGG's internal annotation tool for K number assignment of KEGG GENES using SSEARCH computation]]> KOALA (KEGG Orthology And Links Annotation) is KEGG's internal annotation tool for K number assignment of KEGG GENES using SSEARCH computation. BlastKOALA and GhostKOALA assign K numbers to the user's sequence data by BLAST and GHOSTX searches, respectively, against a nonredundant set of KEGG GENES. Annotate Sequence in KEGG Mapper and Pathogen Checker in KEGG Pathogen are special interfaces to the BlastKOALA server and can be executed in an interactive mode.    See Step-by-step Instructions.

Reference: Kanehisa, M., Sato, Y., and Morishima, K. (2016) BlastKOALA and GhostKOALA: KEGG tools for functional characterization of genome and metagenome sequences. J. Mol. Biol. 428, 726-731. [pubmed] [pdf]

Address of the bookmark: https://www.kegg.jp/blastkoala/

]]> Abhimanyu Singh https://bioinformaticsonline.com/blog/view/37396/converting-a-vcf-into-a-fasta-given-some-reference Fri, 20 Jul 2018 10:03:53 -0500 https://bioinformaticsonline.com/blog/view/37396/converting-a-vcf-into-a-fasta-given-some-reference <![CDATA[Converting a VCF into a FASTA given some reference !]]> Samtools/BCFtools (Heng Li) provides a Perl script vcfutils.pl which does this, the function vcf2fq (lines 469-528)

This script has been modified by others to convert InDels as well, e.g. this by David Eccles

./vcf2fq.pl -f <input.fasta> <all-site.vcf> > <output.fastq>

https://github.com/gringer/bioinfscripts/blob/master/vcf2fq.pl

https://github.com/lh3/samtools/blob/master/bcftools/vcfutils.pl

]]> Jit https://bioinformaticsonline.com/bookmarks/view/44320/tools-for-id-conversion Sat, 20 May 2023 21:53:32 -0500 https://bioinformaticsonline.com/bookmarks/view/44320/tools-for-id-conversion <![CDATA[Tools for id conversion]]> g:Convert enables to convert between various gene, protein, microarray probe and numerous other types of namespaces. We provide at least 40 types of IDs for more than 60 species. The 98 different namespaces supported for human include Ensembl, Refseq, Illumina, Entrezgene and Uniprot identifiers. All namespaces are obtained through matching them via Ensembl gene identifiers as a reference.

Address of the bookmark: https://biit.cs.ut.ee/gprofiler/convert

]]> LEGE https://bioinformaticsonline.com/bookmarks/view/43583/pango-lineage-analysis Mon, 15 Nov 2021 03:38:29 -0600 https://bioinformaticsonline.com/bookmarks/view/43583/pango-lineage-analysis <![CDATA[Pango Lineage Analysis !]]> 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 researchers to perform analyses on SARS-COV-2 sequence data.

Address of the bookmark: https://cov-lineages.org/resources/pangolin/output.html

]]> Abhi https://bioinformaticsonline.com/videolist/watch/4193/bioinformatics-101-running-blast Tue, 03 Sep 2013 14:59:50 -0500 https://bioinformaticsonline.com/videolist/watch/4193/bioinformatics-101-running-blast <![CDATA[Bioinformatics 101 - Running BLAST]]> How to format the database for BLAST, run the command, view the output file, and use BioPerl and Perl to parse the output. By David Francis, Ohio State University. Delivered live at the Tomato Disease Workshop 2010. For more information, please visit http://www.extension.org/pages/32521/bioinformatics-101-video.]]> https://bioinformaticsonline.com/videolist/watch/4851/blast Wed, 25 Sep 2013 10:56:23 -0500 https://bioinformaticsonline.com/videolist/watch/4851/blast <![CDATA[BLAST]]> Dr. Rob Edwards describes how BLAST works]]> https://bioinformaticsonline.com/bookmarks/view/30976/brig Thu, 16 Feb 2017 13:14:25 -0600 https://bioinformaticsonline.com/bookmarks/view/30976/brig <![CDATA[BRIG]]> BRIG is a free cross-platform (Windows/Mac/Unix) application that can display circular comparisons between a large number of genomes, with a focus on handling genome assembly data. The application is available at:http://sourceforge.net/projects/brig

If you have any questions or comments, post them on one of the trackers on BRIG’s SourceForge page:http://sourceforge.net/tracker/?group_id=328245.

Features:

  • Images show similarity between a central reference sequence and other sequences as concentric rings.
  • BRIG will perform all BLAST comparisons and file parsing automatically via a simple GUI.
  • Contig boundaries and read coverage can be displayed for draft genomes; customized graphs and annotations can be displayed.
  • Using a user-defined set of genes as input, BRIG can display gene presence, absence, truncation or sequence variation in a set of complete genomes, draft genomes or even raw, unassembled sequence data.
  • BRIG also accepts SAM-formatted read-mapping files enabling genomic regions present in unassembled sequence data from multiple samples to be compared simultaneously

 

Address of the bookmark: http://brig.sourceforge.net/

]]> Jit https://bioinformaticsonline.com/bookmarks/view/37545/ncbi-magic-blast Tue, 14 Aug 2018 18:11:11 -0500 https://bioinformaticsonline.com/bookmarks/view/37545/ncbi-magic-blast <![CDATA[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 the score of all exons. This is very different from other versions of BLAST, where each exon is scored as a separate hit and read-pairing is ignored.

Magic-BLAST incorporates within the NCBI BLAST code framework ideas developed in the NCBI Magic pipeline, in particular hit extensions by local walk and jump (http://www.ncbi.nlm.nih.gov/pubmed/26109056), and recursive clipping of mismatches near the edges of the reads, which avoids accumulating artefactual mismatches near splice sites and is needed to distinguish short indels from substitutions near the edges.

 

Address of the bookmark: https://ncbi.github.io/magicblast/

]]> Jit https://bioinformaticsonline.com/bookmarks/view/41482/magic-blast Fri, 20 Mar 2020 15:18:36 -0500 https://bioinformaticsonline.com/bookmarks/view/41482/magic-blast <![CDATA[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 the score of all exons. This is very different from other versions of BLAST, where each exon is scored as a separate hit and read-pairing is ignored.

Address of the bookmark: https://ncbi.github.io/magicblast/

]]> Shruti Paniwala