BLAST (Basic Local Alignment Search Tool)

Description

BLAST (Basic Local Alignment Search Tool) finds regions of similarity between biological sequences. BLAST includes several specialized search interfaces: SmartBLAST, Primer-BLAST, Global Align, CD-Search, IgBLAST, VecScreen, CDART, Multiple Alignment, MOLE-BLAST, Searches at a Cloud Provider, BLAST+ Docker Image

Resources

Name Format Description Link
21 Find sequences with similar conserved domain architecture https://www.ncbi.nlm.nih.gov/Structure/lexington/lexington.cgi?cmd=rps
21 http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=Download
21 Find proteins highly similar to your query https://blast.ncbi.nlm.nih.gov/smartblast/?LINK_LOC=BlastHomeLink
21 Design primers specific to your PCR template https://www.ncbi.nlm.nih.gov/tools/primer-blast/index.cgi?LINK_LOC=BlastHome
21 Find conserved domains in your sequence https://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi
21 Search immunoglobulins and T cell receptor sequences https://www.ncbi.nlm.nih.gov/igblast/
21 Align sequences using domain and protein constraints https://www.ncbi.nlm.nih.gov/tools/cobalt/cobalt.cgi?LINK_LOC=BlastHomeLink
21 Establish taxonomy for uncultured or environmental sequences https://blast.ncbi.nlm.nih.gov/moleblast/moleblast.cgi
21 Compare two sequences across their entire span (Needleman-Wunsch) https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastSearch&PROG_DEF=blastn&BLAST_PROG_DEF=blastn&BLAST_SPEC=GlobalAln&LINK_LOC=BlastHomeLink
21 This repository contains documentation for the NCBI BLAST+ command line applications in a Docker image. We will demonstrate how to use the Docker image to run BLAST analysis on the Google Cloud Platform (GCP) and Amazon Web Services (AWS) using a small basic example and a more advanced production-level example. Some basic knowledge of Unix/Linux commands and BLAST+ is useful in completing this tutorial. https://github.com/ncbi/blast_plus_docs
21 Resources include: BLAST+ in a Docker image – How to setup and run BLAST+ via Docker. Database information – How to obtain BLAST databases. BLAST+ user manual - How to run stand-alone BLAST searches. BLAST+ cloud guide - Tutorial with Jupyter Notebooks and Command Line. BLAST+ with Jupyter Notebooks - Designing Educational Experiences. ElasticBLAST - Cloud-based tool to run BLAST searches for large number of queries. https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=CloudBlast
21 Search sequences for vector contamination https://www.ncbi.nlm.nih.gov/tools/vecscreen/
21 Blast.cgi http://blast.ncbi.nlm.nih.gov/Blast.cgi
21 http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=DeveloperInfo
21 downloadblastdata.html https://blast.ncbi.nlm.nih.gov/doc/blast-help/downloadblastdata.html#databases

Tags

  • biotechnology
  • tools-utilities
  • biochemistry
  • computational-biology
  • protein
  • dataset
  • api

Topics

Categories