16S rRNA Refseq V15.22 Genomic RefSeq V9.14
HOMD User Documentation     
Table of Content:
User Documentation
+Taxon Description
+Identify 16S rRNA Sequence
+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
  >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
Search Documentation:
Input Keywords:
Title Content
4-4] BLAST Search main parameters
Restricts the number of short descriptions of matching sequences reported to the number specified; default limit is 100 descriptions. See also EXPECT.
Restricts database sequences to the number specified for which high-scoring segment pairs (HSPs) are reported; the default limit is 100. If more database sequences than this happen to satisfy the statistical significance threshold for reporting (see EXPECT below), o要ly the matches ascribed the greatest statistical significance are reported.
The statistical significance threshold for reporting matches against database sequences; the default value is 10, such that 10 matches are expected to be found merely by chance, according to the stochastic model of Karlin and Altschul (1990). If the statistical significance ascribed to a match is greater than the EXPECT threshold, the match will not be reported. Lower EXPECT thresholds are more stringent, leading to fewer chance matches being reported. Fractional values are acceptable.
The statistical significance threshold for including a sequence in the model used by PSI-BLAST o要 the next iteration.
Enter the organism name in the form "Genus species" (e.g., "Homo sapiens"). A number of popular organism names are listed o要 a pull-down menu.
Enter any taxonomic group from the NCBI taxonomy (e.g. "Mammalia").
Some popular groups are: Archaea Bacteria Eukaryota Embryophyta (higher plants) Fungi Metazoa     (multicellular animals) Vertebrata Mammalia Rodentia Primates
Explore the taxonomy database at NCBI
FILTER (Low-complexity)
Mask off segments of the query sequence that have low compositional complexity, as determined by the SEG program of Wootton & Federhen (Computers and Chemistry, 1993) or, for BLASTN, by the DUST program of Tatusov and Lipman (in preparation). Filtering can eliminate statistically significant but biologically uninteresting reports from the blast output (e.g., hits against common acidic-, basic- or proline-rich regions), leaving the more biologically interesting regions of the query sequence available for specific matching against database sequences. Filtering is o要ly applied to the query sequence (or its translation products), not to database sequences. Default filtering is DUST for BLASTN, SEG for other programs. It is not unusual for nothing at all to be masked by SEG, when applied to sequences in SWISS-PROT, so filtering should not be expected to always yield an effect. Furthermore, in some cases, sequences are masked in their entirety, indicating that the statistical significance of any matches reported against the unfiltered query sequence should be suspect.
FILTER (Human repeats)
This option masks Human repeats (LINE's and SINE's) and is especially useful for human sequences that may contain these repeats. This option is still experimental and under development, so it may change in the near future.
FILTER (Mask for lookup table o要ly)
This option masks o要ly for purposes of constructing the lookup table used by BLAST. The BLAST extensions are performed without masking. This option is still experimental and may change in the near future.
Causes NCBI gi identifiers to be shown in the output, in addition to the accession and/or locus name.
Query Genetic Code
Genetic code to be used in blastx translation of the query.
Graphical Overview
An overview of the database sequences aligned to the query sequence is shown. The score of each alignment is indicated by o要e of five different colors, which divides the range of scores into five groups. Multiple alignments o要 the same database sequence are connected by a striped line. Mousing over a hit sequence causes the definition and score to be shown in the window at the top, clicking o要 a hit sequence takes the user to the associated alignments.
Article last modified on 2014-04-08 11:00:47 by lyang; viewed 1933 times; Category: User Documentation; Topic: Tools & Downloa
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