16S rRNA Refseq V15.22 Genomic RefSeq V9.14
HOMD User Documentation     
Table of Content:
User Documentation
+Overview
+Taxon Description
+Identify 16S rRNA Sequence
+Genomes
+Tools & Download
 >Genomics Tools Overview
 >HOMD Genome Viewer
 >HOMD JBrowse Genome Viewer
 >Dynamic Genome Annotation
 +Blast against Genomes
  >BLAST databases
  >BLAST Search main parameters
  >FASTA format description
  >Full list of the BLAST Advanced options
  >Matrix
  >Out-Of-Frame BLAST notation
  >BLAST Color schema description
  >Programs available for the BLAST search
  >Low complexity filtering
 >HOMD Dynamic Genomic BLAST
 >KEGG Pathway
 >Gene Ontology
 >Sequence Batch Download
+Database Search
General Documentation
+HOMD Information
+Announcement
 
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4-94] Programs available for the BLAST search
The NCBI BLAST family of programs includes:

BLASTPCompares an amino acid query sequence against a protein sequence database
BLASTNCompares a nucleotide query sequence against a nucleotide sequence database
BLASTXCompares a nucleotide query sequence translated in all reading frames against a protein sequence database
TBLASTN Compares a protein query sequence against a nucleotide sequence database dynamically translated in all reading frames
TBLASTXCompares the six-frame translations of a nucleotide query sequence against the six-frame translations of a nucleotide sequence database. Please note that tblastx program cannot be used with the nr database on the BLAST Web page
MegaBLAST Compares a query to closely related sequences and works best if the target percent identity is 95% or more but is very fast
Discontiguous MegaBLASTUses an initial seed that ignores some bases (allowing mismatches) and is intended for cross-species comparisons
PSI-BLAST Allows the user to build a PSSM (position-specific scoring matrix) using the results of the first BlastP run
PHI-BLAST Performs the search but limits alignments to those that match a pattern in the query
DELTA-BLAST Constructs a PSSM using the results of a Conserved Domain Database search and searches a sequence database

Article last modified on 2015-09-15 11:08:27 by tsute; viewed 1001 times; Category: User Documentation; Topic: Tools & Downloa
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