BLAST searches

However, the PSI-BLAST search method, using a very conservative inclusion threshold of E < 10 4, can detect, with significance, the similarities in sequence between previously known VWA domains and integrin /3 subunits (Table II). The hypothesis that all integrin [3 subunits contain a VWA domain appears to be correct. 

We performed a benchmark analysis on a set of genes for which the full mRNA and/or the pertinent protein sequence was documented in the literature. Instead of clustering ESTs without any template, we aligned them by a BLAST search (Altshul et al., 1997) to this set of master mRNA sequences and looked in these alignments for variant letters. We applied a set of filters as follows ... 

The BLAST searching output can help users deduce functional and evolutionary information for their query sequences. BLAST can also be used for comparisons in certain categories, such as SNP BLAST and Immunoglobin BLAST (IgBlast). 

A characterization of the translocase complexes responsible for mitosomal protein import in Giardia is under way. An iterative BLAST search of the G. intestinalis genome was employed for the identification of the import machinery components. The only candidate to have been found so far is GiPAMIS, a mitosomal protein homologous to mitochondrial presequence translocase-associated motor 18 (Dolezal et al. 2005). 

Another useful structure tool is RasMol (or RasMac). This will allow you to view the detailed structure of a protein and rotate it on coordinates so you can see it from all perspectives. A hyperlink to RasMol is present under the View Structure function just above Chime. You may need to study RasMol instructions provided under Help, or you may use a Ra.s Mol tutorial listed in Table El.2. Another useful protein viewer is tin-Swiss-Protein Pdv Viewer (Table El.2). BLAST is an advanced sequence similarity tool available at NCBI. To access this, go to the NCBI home page (www.ncbi.nlm.nih.gov) and click on BLAST. Then click on Basic BLAST search to obtain a dialogue box into which you may type the amino acid sequence of human a-lactalbumin. This process may be stream lined by downloading the amino acid sequence in FASTA format into a file and transferring the fde into the BLAST dialogue box. BLAST will provide a list of proteins with sequences similar to the one entered. 

Study the nucleotide sequence for the gene coding for human a-lactalbumin. Hint Begin at the NCBI home page and enter Entrez. Click on Nucleotides and do a search on human a-lactalbumin. Review the GenBank report for the position of introns and exons. Obtain a FASTA report, transfer (download) the files, and complete a BLAST search for related sequences. 

Data gathering was through BLAST search in SwissProt (Peitsch, 1995,1996). 

Blasting nucleotide sequences is not always that easy, because there is more ambiguity to the nucleotide sequence, and good hits have to have a 70% homology over the whole sequence to be reliable, compared to 25% with proteins. If the coding region is known, it is better to translate the nucleotide sequence into protein and then start a blast search. 

Using a variety of known short-chain alcohol dehydrogenases as probes for BLAST searching of the yeast genome revealed an additional eight putative pro-... 

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