IBISS: Interactive Bovine In Silico SNP Database

How To Use IBISS

The database can be searched in a number of ways:

Typical IBISS Page

Link Descriptions

MSF:Multiple Sequence File
Contig View:A view of how the sequences in the contig align.
Consensus:The consensus sequence in fasta format
Library:Any information relating to the tissue, library and species that was sequenced for any/all of the sequences in that contig
NetBlast:If You wish to do a netblast against genbank non redundant database
ESTScan:Output to determine the amino acid sequence. We use this when the Fasty search does not return a good hit.
Nap:The output of the nap programs which aligns an amino acid sequence back to the DNA sequence
SBSn:Blat alignment of bovine nucleotide with the human chromosome DNA sequence
SBSp:Blat output from the bovine sequence translated in six fames and aligned with the human sequence, translated in six frames
HSA:A table showing all the bovine genes in IBISS listed from one end of the human chromosomes to the other
Gbrowse:Consensus and singleton sequences displayed in the Generic Genome Browser

Searching IBISS using a key word

A search index was created from all blast hits of bovine consensus sequences and singletons to the human nucleotide and protein sequences that displayed an e value less than 1e-30 but no more than 15 hits per blast search. A keyword search looks through that search index to find the term entered. IMPORTANT: This term may not be found in the best hit for a particular sequence. Instead, it may be far down the list of entries. For example, a keyword search using 'gstm3' returns two hits as shown in this image:

The first hit is in btcn6520. As you can see from the results, this hit against gstm3 was 9th in that particular blast file, with an e value of 1e-31. You could go to this btcn and verify that the top hit for this sequences is not gstm3. In fact, for this btcn sequence, the top hit is gstm5, not gstm3. The second result (btcn14808) shows an e value of 0 to human gstm3 and this hit is the first (top hit) of this consensus sequence against the human gstm3 gene. This result is more significant than the previous one. Most keyword searches are far more complex than this example so it is very important to understand that not all search results correspond to top hits.