Using Genomic BLAST.
Genomic BLAST pages are helpful because they allow the genomic context of a BLAST search to be displayed in the Map Viewer. For example, discontiguous (cross-species) MegaBLAST against the human...
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How to do Batch BLAST jobs.
BLAST makes it easy to examine a large group of potential gene candidates. Most likely these are isolated as amplified products from a library of some sort. There is no need to manually cut and paste...
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How to Search Custom Databases in Web-Blast Using Entrez Queries.
A powerful feature of the BLAST Web interface is the ability to limit BLAST searches to a subset of any database using a standard Entrez query. Skillful use of Entrez queries allows the equivalent of...
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Use Genomic BLAST to see the genomic context
If you are interested in the evolution of a particular gene or gene family it is often intetesting to examine the intro-exon structure even across species. Often, the only data available is the mRNA...
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How to save custom search pages.
So you have made a few BLAST searches and after adjusting the database, organism limits and maybe a few Algorithm Parameters you arrive at what you think is a good search strategy. Do you want to have...
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Using Tree View to Examine Relationships Between Sequences.
The new Tree View option on the NCBI Web BLAST service presents a dendrogram or tree display that clusters sequences according to their distances from the query sequence. This display is helpful for...
View ArticleIntegrating web PSI-BLAST with command line PSI-BLAST using the...
This format of the PSSM can be directly used with other stand-alone Blast software tools, in particular as an input checkpoint file for blastpgp. The actual matrix elements can be observed in the...
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