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
 
Search Documentation:
Input Keywords:
Title Content
4-93] Out-Of-Frame BLAST notation
When protein aligned to the nucleotide there are 6 possibilities of match at any point. In OOF alignment - upper sequence is DNAP - 3 frame translated DNA. Lower sequence is protein. At any position next protein base may be aligned to 6 possible bases in DNAP:

(TBO - traditional blast output)

0:         3 nucleotides missing - gap (TBO notation "-")

OOF alignment with DNAP:        DTRGGDTPQKSVFSRAQNTLWGERGDTQKRGGAQRGDIFSLWGG-GVLCV       |  |  |  |  |  |  |  |  |  |  |  |  |  |  |   |  |       D  G  T  K  F  A  T  G  G  Q  G  Q  D  S  G K V  V  TBO:        DGTKFATGGQGQDSG-VV       DGTKFATGGQGQDSG VV       DGTKFATGGQGQDSGKVV 
1:         2 nucleotides missing - "frameshift -2" (TBO notation "\\")
OOF alignment with DNAP:        DTRGGDTPQKSVFSRAQNTLWGERGDTQKRGGAQRGDIFSLWGGGGVLCV       |  |  |  |  |  |  |  |  |  |  |  |  |  |  |/  |  |       D  G  T  K  F  A  T  G  G  Q  G  Q  D  S  GK  V  V  TBO:        DGTKFATGGQGQDSG\\GVV       DGTKFATGGQGQDSG   VV       DGTKFATGGQGQDSG  KVV 
2:         1 nucletide missing - "frameshift -1" (TBO notation "\")
OOF alignment with DNAP:        DTRGGDTPQKSVFSRAQNTLWGERGDTQKRGGAQRGDIFSLWGGERGV       |  |  |  |  |  |  |  |  |  |  |  |  |  | /  |  |         D  G  T  K  F  A  T  G  G  Q  G  Q  D  S G  K  V   TBO:        DGTKFATGGQGQDS\GEV       DGTKFATGGQGQDS G V       DGTKFATGGQGQDS GKV   
3:         Complete match
OOF alignment with DNAP:        DTRGGDTPQKSVFSRAQNTLWGERGDTQKRGGAQRGDIFSLWGGEKRGV       |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |        D  G  T  K  F  A  T  G  G  Q  G  Q  D  S  G  K  V   TBO:        DGTKFATGGQGQDSGKV       DGTKFATGGQGQDSGKV        DGTKFATGGQGQDSGKV  
4:         1 nucleotide insertion - "frameshift +1" (TBO notation "/")
OOF alignment with DNAP:        DTRGGDTPQKSVFSRAQNTLWGERGDTQKRGGAQRGDIFSLWGGVEKRGV       |  |  |  |  |  |  |  |  |  |  |  |  |  |  |   \       D  G  T  K  F  A  T  G  G  Q  G  Q  D  S  G   K  V  TBO:        DGTKFATGGQGQDSG/KV       DGTKFATGGQGQDSG KV       DGTKFATGGQGQDSG KV 
5:         2 nucleotides insertion - "frameshift +2" (TBP notation "//")
OOF alignment with DNAP:        DTRGGDTPQKSVFSRAQNTLWGERGDTQKRGGAQRGDIFSLFLWGGEKRGV       |  |  |  |  |  |  |  |  |  |  |  |  |  |    \  |  |       D  G  T  K  F  A  T  G  G  Q  G  Q  D  S    G  K  V  TBO:        DGTKFATGGQGQDS//GKV       DGTKFATGGQGQDS  GKV       DGTKFATGGQGQDS  GKV 
Article last modified on 2014-04-08 11:01:19 by lyang; viewed 2590 times; Category: User Documentation; Topic: Tools & Downloa
Copyright 2007-2022 The Forsyth Institute
Hosted on Amazon AWS EC2
192.168.0.51