<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/16685?offset=30 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 https://bioinformaticsonline.com/news/view/44604/new-release-of-refseq Tue, 16 Jul 2024 10:09:21 -0500 https://bioinformaticsonline.com/news/view/44604/new-release-of-refseq <![CDATA[New Release of RefSeq !]]> Check out RefSeq release 225, now available online and from the FTP site. You can access RefSeq data through NCBI Datasets.

What’s included in this release?

As of July 8, 2024, this full release incorporates genomic, transcript, and protein data containing:

  • 448,507,905 records
  • 334,845,613 proteins
  • 63,542,774 RNAs
  • Sequences from 152,668 organisms

The release is provided in several directories as a complete dataset and also as divided by logical groupings.

]]> Abhi https://bioinformaticsonline.com/bookmarks/view/42572/the-breeding-api-brapi-project Wed, 06 Jan 2021 19:51:17 -0600 https://bioinformaticsonline.com/bookmarks/view/42572/the-breeding-api-brapi-project <![CDATA[The Breeding API (BrAPI) project]]> The Breeding API (BrAPI) project is an effort to enable interoperability among plant breeding databases. BrAPI is a standardized RESTful web service API specification for communicating plant breeding data. This community driven standard is free to be used by anyone interested in plant breeding data management.

Address of the bookmark: https://brapi.org/

]]> BioStar https://bioinformaticsonline.com/bookmarks/view/19636/google-genomics Thu, 18 Dec 2014 11:05:42 -0600 https://bioinformaticsonline.com/bookmarks/view/19636/google-genomics <![CDATA[Google Genomics]]>

  • Explore genetic variation interactively. Compare entire cohorts in seconds with SQL-like queries. Compute transition/transversion ratios, genome-wide association, allelic frequency and more.

  • Process big genomic data easily. Run batch analyses like principal component analysis and Hardy-Weinberg equilibrium on as many samples as you like, in minutes or hours, with just a little code.

  • Use Google's infrastructure and big data expertise. Store one genome or a million using Google Genomics and take advantage of the same infrastructure that powers Search, Maps, YouTube, Gmail and Drive.

  • Support emerging global standards. Google Genomics is implementing the API defined by the Global Alliance for Genomics and Health for visualization, analysis and more. Compliant software can access Google Genomics, local servers, or any other implementation.

    • Address of the bookmark: https://cloud.google.com/genomics/

    ]]>     Tenzin Paul     https://bioinformaticsonline.com/bookmarks/view/40786/google-colab-google-colab-is-a-free-cloud-service-and-now-it-supports-free-gpu Fri, 31 Jan 2020 01:31:23 -0600 https://bioinformaticsonline.com/bookmarks/view/40786/google-colab-google-colab-is-a-free-cloud-service-and-now-it-supports-free-gpu <![CDATA[Google Colab : Google Colab is a free cloud service and now it supports free GPU!]]> You can: improve your Python programming language coding skills. develop deep learning applications using popular libraries such as Keras, TensorFlow, PyTorch, and OpenCV. 

    If you have just a single notebook to submit, use the website https://google-colab.com/, it is really easy, on the top right corner click 'submit +'. The earlier you post the more visibility you will get over time

    Address of the bookmark: http://colab.research.google.com

    ]]>     Jit     https://bioinformaticsonline.com/blog/view/40953/explore-taxdump-files Sat, 08 Feb 2020 04:44:55 -0600 https://bioinformaticsonline.com/blog/view/40953/explore-taxdump-files <![CDATA[Explore taxdump files !]]> This is an extract of taxdump-readme.txt to be found at ftp://ftp.ncbi.nih.gov/pub/taxonomy/ The content of the archive -------------------------- It may look like this: delnodes.dmp division.dmp gencode.dmp merged.dmp names.dmp nodes.dmp readme.txt The readme.txt file gives a brief description of *.dmp files. These files contain taxonomic information and are briefly described below. Each of the files store one record in the single line that are delimited by "\t|\n" (tab, vertical bar, and newline) characters. Each record consists of one or more fields delimited by "\t|\t" (tab, vertical bar, and tab) characters. The brief description of field position and meaning for each file follows. nodes.dmp --------- This file represents taxonomy nodes. The description for each node includes the following fields: tax_id -- node id in GenBank taxonomy database parent tax_id -- parent node id in GenBank taxonomy database rank -- rank of this node (superkingdom, kingdom, ...) embl code -- locus-name prefix; not unique division id -- see division.dmp file inherited div flag (1 or 0) -- 1 if node inherits division from parent genetic code id -- see gencode.dmp file inherited GC flag (1 or 0) -- 1 if node inherits genetic code from parent mitochondrial genetic code id -- see gencode.dmp file inherited MGC flag (1 or 0) -- 1 if node inherits mitochondrial gencode from parent GenBank hidden flag (1 or 0) -- 1 if name is suppressed in GenBank entry lineage hidden subtree root flag (1 or 0) -- 1 if this subtree has no sequence data yet comments -- free-text comments and citations names.dmp --------- Taxonomy names file has these fields: tax_id -- the id of node associated with this name name_txt -- name itself unique name -- the unique variant of this name if name not unique name class -- (synonym, common name, ...) division.dmp ------------ Divisions file has these fields: division id -- taxonomy database division id division cde -- GenBank division code (three characters) division name -- e.g. BCT, PLN, VRT, MAM, PRI... comments gencode.dmp ----------- Genetic codes file: genetic code id -- GenBank genetic code id abbreviation -- genetic code name abbreviation name -- genetic code name cde -- translation table for this genetic code starts -- start codons for this genetic code delnodes.dmp ------------ Deleted nodes (nodes that existed but were deleted) file field: tax_id -- deleted node id merged.dmp ---------- Merged nodes file fields: old_tax_id -- id of nodes which has been merged new_tax_id -- id of nodes which is result of merging ]]> Jit https://bioinformaticsonline.com/news/view/5887/pubmed-opens-for-comment Thu, 24 Oct 2013 12:40:17 -0500 https://bioinformaticsonline.com/news/view/5887/pubmed-opens-for-comment <![CDATA[PubMed opens for comment]]> The informal conversations that researchers have at scientific meetings look set to move online, if a new initiative by the US National Center for Biotechnology Information (NCBI) has its way. On 22 October, the NCBI of Bethesda, Maryland, launched the pilot phase of a programme called PubMed Commons. This will allow users to comment on published abstracts on the PubMed website, which indexes some 22 million papers.

    For now, only a select group of researchers and their invited guests can use the system. But the NCBI's director David Lipman, who helped to develop the programme, says that soon any PubMed author will be allowed to comment under his or her real name and anyone will be able to read the comments.

    More @ http://www.nature.com/news/pubmed-opens-for-comment-1.14023

    News source Nature.

    ]]>     Rahul Nayak     https://bioinformaticsonline.com/videolist/watch/16686/sequence-viewer-download-transcripts-exons-and-proteins Mon, 15 Sep 2014 17:30:36 -0500 https://bioinformaticsonline.com/videolist/watch/16686/sequence-viewer-download-transcripts-exons-and-proteins <![CDATA[Sequence Viewer: Download Transcripts, Exons and Proteins]]> How to download FASTA sequence for certain gene features while in the NCBI's Sequence Viewer. Sequence Viewer homepage: www.ncbi.nlm.nih.gov/projects/sviewer/ Sequence Viewer playlist: https://www.youtube.com/playlist?list=PL76D7EE6A6A8AC1C3]]> https://bioinformaticsonline.com/bookmarks/view/27691/histonedb-20-%E2%80%93-with-variants Fri, 03 Jun 2016 05:06:20 -0500 https://bioinformaticsonline.com/bookmarks/view/27691/histonedb-20-%E2%80%93-with-variants <![CDATA[HistoneDB 2.0 – with variants]]> This histone database can be used to explore the diversity of histone proteins and their sequence variants in many organisms. The resource was established to better understand how sequence variation may affect functional and structural features of nucleosomes. To get started, select a histone type to explore its variants.

    More at http://www.ncbi.nlm.nih.gov/projects/HistoneDB2.0/index.fcgi/browse/

    Address of the bookmark: http://www.ncbi.nlm.nih.gov/projects/HistoneDB2.0/index.fcgi/browse/

    ]]>     Anjana