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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4-1] Blast against Genomes
HOMD provides sequence homology searches against all the human oral microbial sequences using NCBI's BLAST Search program. Searches can be done against each genome individually or the combination of all genomes that are being curated and annotated at HOMD. For each genome or the combined sequences, searches can be done against three different subsets of these sequences: 1. The total nucleotide sequences, e.g., the entire genomic sequences including chromosome and plasmids (if the genome is completed sequenced) or the contig sequences (if partially sequenced). Search can be done with NCBI's BLASTN, TBLASTX, and TBLASTN. 2. The nucleotide sequences of all the open reading frames (ORFs) found in the individual or combined genomes. BLASTN, tBLASTX, and TBLASTN can be done against these sequence sets. 3. The amino acid sequences of all the ORFs found in the individual or combined genomes. BLASTP and BLASTX can be used in this case.The BLAST search page can be access either by selecting the genome first from one of the six Genome Tables or by selecting the "BLAST against Genomes" menu from the top or side menu. Note that this BLAST search is different from the Identify 16S rRNA Sequence option, in that searches are only against the 16S rRNA sequences.Below is a screen shot of the BLAST page. Documentations are available for each facets of the BLAST program including type of programs, databases, sequence format and parameters, etc. They can be conveniently accessed by following the link provided in this page. To use the BLAST, first copy and paste your sequence in FASTA format into the sequence box, or upload from your computer using the "Browse" button. Then select a program (e.g., BLASTN or BLASTP, etc) and then a separate menu will show up to indicate which subset of sequences are available for search against the input sequences.
Article last modified on 2014-04-08 11:00:02 by lyang; viewed 28499 times; Category: User Documentation; Topic: Tools & Downloa

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