You are able to access a variety of sequence analysis tools directly from the sequence information sections of ZFIN. The analysis tools available for each sequence are listed in a pulldown menu in the far right column of the sequence information section on Gene, Marker and Clone pages. When only one analysis tool is available for a sequence, a button replaces the pulldown menu.

Analysis tools available for sequences in ZFIN are:

ZFIN BLAST – ZFIN BLAST uses WU-BLAST to compare the search sequence with a variety of nucleotide and protein sequence datasets. These include GenBank zebrafish mRNA, DNA, EST and protein sequences. ZFIN BLAST also offers the advantage of integration with the ZFIN database and searches with ZFIN specific sequence data sets returns BLAST results that allow direct navigation to gene and clone pages in ZFIN.Additional sequence sets include curated Vega transcripts, Ensembl transcripts, TIGR zebrafish clusters.

NCBI BLAST – The Basic Local Alignment Search Tool (BLAST) is used to compare nucleotide or amino acid sequences for identity and similarity with other sequences. Selecting this tool opens a search form for a BLAST analysis at the National Center for Biotechnology Information (NCBI). The sequence accession number of interest is automatically added to the search form for your convenience. Just select your search options and click the BLAST! button on the NCBI page.

Ensembl – Selecting this tool opens a search form for a BLAST analysis at The Wellcome Trust Sanger Institute’s Ensembl BLASTView resource. The sequence accession number of interest is automatically added to the search form for your convenience. Just select your search options and click the RUN button near the bottom of the Sanger BLASTView page.

Mega BLAST – Mega BLAST is a BLAST algorithm that more efficiently handles longer nucleotide sequences. Selecting this tool opens a search form for a Mega BLAST analysis at the National Center for Biotechnology Information. The sequence accession number of interest is automatically added to the search form for your convenience. Just select your search options and click the BLAST! button on the NCBI page.

SIB BLAST – Selecting this tool runs an amino acid sequence BLAST analysis at Swiss Institute of Bioinformatics (SIB). The results are automatically displayed on the SIB page.

UCSC BLAT – The Blast-Like Alignment Tool (BLAT) is genome browser that displays the sequence of interest in the context of other genome features such as known genes from a number of species, other nucleotide sequences, and gene prediction models. Selecting this tool runs a BLAT analysis against the Santa Cruz (UCSC) Genome Bioinformatics Site. The results are automatically displayed on the UCSC page.