Help:BLAST Search

From Human Salivary Proteome Wiki

BLAST Search

The Basic Local Alignment Search Tool (BLAST) finds regions of local similarity between sequences, the result of which can be used to infer functional and evolutionary relationships. The BLAST tool on the Human Salivary Proteome Wiki uses Position-Specific Iterated (PSI)-BLAST. It is the most sensitive BLAST program, making it useful for finding very distantly related proteins or new members of a protein family. The tool compares protein sequence input to the sequences in the International Protein Index (IPI) database and calculates the statistical significance of matches.

The BLAST search facility on the wiki is provided by the European Bioinformatics Institute (EBI). Currently, only default parameters are allowed when submitting a job from the wiki. Please follow this link to examine the default parameter values and to learn more about the tool. There are two convenient ways to run BLAST on the wiki:

On a protein page

On any protein pages, there is a "BLAST Search" link in the Tools panel, which will let you easily BLAST the canonical sequence of the protein against the IPI protein database. If the protein has multiple isoforms and you want to BLAST a particular one of them, go to the corresponding sequence page by clicking the link for that sequence under the Sequence Attributes section. On the sequence page, just follow the same simple steps described here.

Using the special page

The BLAST special page is useful if you have a novel protein sequence that is not stored on the wiki. Enter or paste the sequence into the text box, as shown in Figure 1, then press Search to submit the run.

Fig. 1: The BLAST Special page where you can enter any amino acid sequence to search against.

Display of Search Results

The result page consists two parts conveying almost the same information using different formats. On top is a graphical representation of the matches (Figure 2). In addition to the list of proteins whose sequences produced significant alignments, each match is accompanied by the relative position of where the sequences align and the Expectation value, which indicates the amount of random background noise.

Fig. 2: The BLAST search result represented in graphical format. The Download XML button lets you save the result in XML format.

At the bottom is the raw search result as shown in Figure 3. The additional information you can see from this representation are match scores and a more detailed pair-wise alignment between each pair of matches. You can also export the entire report in XML format by pressing the "Download XML" button on top of the page (also highlighted in Figure 2).

Fig. 3: The raw BLAST search result showing match scores and pair-wise alignments.

Reference

Altschul SF, et al. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25(17):3389-402 [PubMed:9254694]