Home Search Tools Statistics Ftp Links About Help   
IVDB Sequence Polymorphism

For sequence polymorphism analysis Help


Search Option
     Nucleotide sequence:      Protein sequence:
     Select Host:        
     Select Subtype:  
     Select Segment: 
                    
IVDB provides pre-computed polymorphisms in IV genes and proteins, which are grouped by host, subtype and segment. Users are able to search sequence polymorphisms by host, subtype, and segment. The pre-made alignments, phylogenetic trees, and geographical distributions in a world map are also available for instant access.
     
For Nucleotide Sequence
     
There are two ways to illustrate the sequence polymorphisms. One is the SNP distribution plot and the minor allele distribution plot on each polymorphism site. The other is the consensus sequence with a list of A, T, C, G statistics on each position. SNP is defined as the position which has different nucleoside between sequences. The major allele on SNP position is defined as the nucleoside whose number on position i is the most, the other nucleosides on this position are defined as minor allele. For example, if there are 260 As, 5 Ts and 1 C on position i, the major allele is A, the minor alleles are T and C.
     
For Protein Sequence
     
The distribution of each amino acid on each polymorphic site is shown in tabular list.
     
Further Analysis
     
For sequences you have chosen for polymorphism analysis, we offer tools for further research.
  • Download the alignment result file.
  • Get the corresponding protein polymorphisms from nucleotide sequences, and vice versa.
  • Build phylogenetic tree for these sequences.
  • Draw the data distribution map by using our IV Sequence Distribution Tool.

IVDB is supported by institutional grant from Beijing Institute of Genomics, CAS  Feedback