<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/44370?offset=20 https://bioinformaticsonline.com/news/view/41586/primer-blast Tue, 28 Apr 2020 00:28:49 -0500 https://bioinformaticsonline.com/news/view/41586/primer-blast <![CDATA[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 expression assays. See the NCBI Insights post (https://go.usa.gov/xvUT4) for more details.

 

If you have any questions or concerns, please contact blast-help@ncbi.nlm.nih.govimage

]]> BioStar https://bioinformaticsonline.com/pages/view/37198/understanding-blastn-output-format-6 Wed, 27 Jun 2018 18:38:21 -0500 https://bioinformaticsonline.com/pages/view/37198/understanding-blastn-output-format-6 <![CDATA[Understanding BLASTn output format 6 !]]> BLASTn output format 6
BLASTn maps DNA against DNA, for example gene sequences against a reference genome

blastn  -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 evalue bitscore

 1.  qseqid  query (e.g., gene) sequence id
 2.  sseqid  subject (e.g., reference genome) sequence id
 3.  pident  percentage of identical matches
 4.  length  alignment length
 5.  mismatch  number of mismatches
 6.  gapopen  number of gap openings
 7.  qstart  start of alignment in query
 8.  qend  end of alignment in query
 9.  sstart  start of alignment in subject
 10.  send  end of alignment in subject
 11.  evalue  expect value
 12.  bitscore  bit score


Define your own output format

by adding the option -outfmt, as for example: 

-outfmt "6 qseqid sseqid pident qlen length mismatch gapope evalue bitscore"

supported format specifiers are:
qseqid    Query Seq-id
qgi       Query GI
qacc      Query accesion
qaccver   Query accesion.version
qlen      Query sequence length
sseqid    Subject Seq-id
sallseqid All subject Seq-id(s), separated by a ';'
sgi       Subject GI
sallgi    All subject GIs
sacc      Subject accession
saccver   Subject accession.version
sallacc   All subject accessions
slen      Subject sequence length
qstart    Start of alignment in query
qend      End of alignment in query
sstart    Start of alignment in subject
send      End of alignment in subject
qseq      Aligned part of query sequence
sseq      Aligned part of subject sequence
evalue    Expect value
bitscore  Bit score
score     Raw score
length    Alignment length
pident    Percentage of identical matches
nident    Number of identical matches
mismatch  Number of mismatches
positive  Number of positive-scoring matches
gapopen   Number of gap openings
gaps      Total number of gaps
ppos      Percentage of positive-scoring matches
frames    Query and subject frames separated by a '/'
qframe    Query frame
sframe    Subject frame
btop      Blast traceback operations (BTOP)
staxids   Subject Taxonomy ID(s), separated by a ';'
sscinames Subject Scientific Name(s), separated by a ';'
scomnames Subject Common Name(s), separated by a ';'
sblastnames Subject Blast Name(s), separated by a ';'   (in alphabetical order)
sskingdoms  Subject Super Kingdom(s), separated by a ';'     (in alphabetical order) 
stitle      Subject Title
salltitles  All Subject Title(s), separated by a '<>'
sstrand   Subject Strand
qcovs     Query Coverage Per Subject
qcovhsp   Query Coverage Per HSP

default values are:
-outfmt "6 qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore"

]]> Rahul Nayak https://bioinformaticsonline.com/blog/view/43424/rest-api Mon, 04 Oct 2021 12:46:40 -0500 https://bioinformaticsonline.com/blog/view/43424/rest-api <![CDATA[REST API]]> REST API

The Representational State Transfer (REST) sample clients are provided for a number of programming languages. For details of how to use these clients, download the client and run the program without any arguments.

Language
Download
Requirements
Perl psiblast.pl LWP and XML::Simple

Python

psiblast.py

 xmltramp2

For details see Environment setup for REST Web Services and Examples for Perl REST Web Services Clients pages.

]]> Neel 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/bookmarks/view/38678/upho-scripts-for-homology-and-orthology-assessment-from-genomic-sequences Mon, 14 Jan 2019 10:36:42 -0600 https://bioinformaticsonline.com/bookmarks/view/38678/upho-scripts-for-homology-and-orthology-assessment-from-genomic-sequences <![CDATA[UPhO: Scripts for homology and orthology assessment from genomic sequences.]]> UPhO finds orthologs with and without inparalogs from input gene family trees. Refer to the Documentation.pdf for more detailed explanations on its usage, installation and dependencies. Type UPhO.py -h for help.

The only input requierement for UPhO is a tree (or trees) in Newick format in which the leaves are named with a species idenfifier, a field separator, and sequence identifier. By default, the field separator is the character "|" but custom delimiters can be defined. Examples of trees to test UPhO are provided in the TestData folder.

Address of the bookmark: https://github.com/ballesterus/UPhO

]]> BioStar https://bioinformaticsonline.com/bookmarks/view/40994/biological-databases Wed, 12 Feb 2020 01:16:29 -0600 https://bioinformaticsonline.com/bookmarks/view/40994/biological-databases <![CDATA[Biological databases !]]> Now a days there are a lots of genomics databases available around the world. This bookmark is created to provide all links in one place ...

ftp://ftp.ncbi.nih.gov/genomes/

https://hgdownload.soe.ucsc.edu/downloads.html

Address of the bookmark: ftp://ftp.ncbi.nih.gov/genomes/

]]> BioStar https://bioinformaticsonline.com/news/view/8504/update-genome-workbench-2715-released Wed, 26 Feb 2014 16:12:17 -0600 https://bioinformaticsonline.com/news/view/8504/update-genome-workbench-2715-released <![CDATA[Update Genome Workbench 2.7.15 released]]> NCBI Genome Workbench is an integrated application for viewing and analyzing sequence data. With Genome Workbench, you can view data in publically available sequence databases at NCBI, and mix this data with your own private data.

Introductory screen shot

Genome Workbench can display sequence data in many ways, including graphical sequence views, various alignment views, phylogenetic tree views, and tabular views of data. It can also align your private data to data in public databases, display your data in the context of public data, and retrieve BLAST results.

Genome Workbench is built on the NCBI C++ ToolKit and uses cross-platform APIs for graphics. It runs on your local machine, and is available for Windows 2000/XP, Linux, MacOS X, and various flavors of Unix.

NCBI Genome Workbench is an integrated application for viewing and analyzing sequence data. Genome Workbench was developed entirely in-house at NCBI and makes use of the NCBI C++ ToolKit. The C++ ToolKit provides a convenient and flexible cross-platform API for managing system internals, database connections, network sockets, and the NCBI data model. In addition, the C++ ToolKit provides the Object Manager, which abstracts handling of sequences and sequence-related objects.

 New Features in Genome Workbench 2.7.15

  • Multiple Alignment View: implemented adaptive feature display when zooming in
  • Active Objects Inspector replaces Selection Inspector. New View should offer an improved selection context examination. See Using Active Objects Inspector tutorial for more details.
  • Binary packages for Linux OpenSUSE 13.1 are now available


Bug Fixes and Improvements in Genome Workbench 2.7.15

  • Fixed major issue with OpenGL overlay/scrolling. Could cause crashes or view scrolling irregularities
  • Multiple Pane View: fixed crash on loading BLAST results
  • Graphical Sequence View: fixed crash on zooming in and out, related to SNP track
  • Graphical Sequence View: fixed Go To Position dialog to give better diagnostics in case of a user error
  • Graphical Sequence View: PDF export fixed rendering of Markers with commas in the name
  • Text View / Flat File: fixed Mac OS rendering issues
  • Text View / Flat File: performance optimization, extended capabilities of real-time rendering of molecules to tens of thousands
  • File Import: optimization improvement to speed up load of files containing multiple project items
  • File Import: remapping stage now shows accession.version and description of molecules, instead of plain GI numbers
  • Mac OS: improved tooltips for toolbar buttons
  • Phylogenetic Tree Builder Tool: improved diagnostics of errors
  • Multiple Alignment View: optimizations to avoid main GUI freezes
  • Open Dialog: removed duplicate elements in table of genomes (load Genome)
  • PDF export: fixed issue with XREF table errors
  • Tree View: fixed issues with showing Force Layout progress on Mac OS
  • Tree View: PDF export fixed issues for showing labels of collapsed nodes
  • Tree View: added an option to stop layout
  • Tree View: broadcasting mechanism fixed not to accumulate selected nodes

Reference:

NCBI news

http://www.ncbi.nlm.nih.gov/tools/gbench/

]]> Surabhi Chaudhary https://bioinformaticsonline.com/bookmarks/view/26375/ncbi-remap Thu, 11 Feb 2016 11:02:26 -0600 https://bioinformaticsonline.com/bookmarks/view/26375/ncbi-remap <![CDATA[NCBI Remap]]> NCBI Remap. This tool is conceptually similar to liftOver in that in manages conversions between a pair of genome assemblies but it uses different methods to achieve these mappings. It is also available through a simple web interface or you can use the API for NCBI Remap.

More at http://www.ncbi.nlm.nih.gov/genome/tools/remap

API http://www.ncbi.nlm.nih.gov/genome/tools/remap/docs/api

Address of the bookmark: http://www.ncbi.nlm.nih.gov/genome/tools/remap

]]> Jit https://bioinformaticsonline.com/news/view/27713/mutabind Mon, 06 Jun 2016 13:34:09 -0500 https://bioinformaticsonline.com/news/view/27713/mutabind <![CDATA[MutaBind]]> MutaBind is a new computational method and server created through NCBI research efforts that maps mutations on a protein structural complex, calculates changes in binding affinity, identifies deleterious mutations and produces a downloadable mutant structural model. http://www.ncbi.nlm.nih.gov/projects/mutabind/index.fcgi/

image

MutaBind guides you through this process, step by step, starting with selecting a protein complex and inputting PDB code or uploading PDB files. You can also retrieve results with a job ID number, view help documents, and review the MutaBind method and references.

More at http://www.ncbi.nlm.nih.gov/projects/mutabind/index.fcgi/

]]> Jit https://bioinformaticsonline.com/bookmarks/view/32730/ncbi-prokaryotic-genome-annotation-pipeline Tue, 16 May 2017 08:56:03 -0500 https://bioinformaticsonline.com/bookmarks/view/32730/ncbi-prokaryotic-genome-annotation-pipeline <![CDATA[NCBI Prokaryotic Genome Annotation Pipeline]]> NCBI Prokaryotic Genome Annotation Pipeline is designed to annotate bacterial and archaeal genomes (chromosomes and plasmids).

Genome annotation is a multi-level process that includes prediction of protein-coding genes, as well as other functional genome units such as structural RNAs, tRNAs, small RNAs, pseudogenes, control regions, direct and inverted repeats, insertion sequences, transposons and other mobile elements.

NCBI has developed an automatic prokaryotic genome annotation pipeline that combines ab initio gene prediction algorithms with homology based methods. The first version of NCBI Prokaryotic Genome Automatic Annotation Pipeline (PGAAP; see Pubmed Article) developed in 2005 has been replaced with an upgraded version that is capable of processing a larger data volume. You can find a more detailed description of the new version of the pipeline in NCBI Handbook chapter. NCBI's annotation pipeline depends on several internal databases and is not currently available for download or use outside of the NCBI environment.

https://www.ncbi.nlm.nih.gov/genome/annotation_prok/

Address of the bookmark: https://www.ncbi.nlm.nih.gov/genome/annotation_prok/

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