Blast and CulstalW tutorials

Blast and CulstalW tutorials - BLAST Input: Select a search...

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http://blast.ncbi.nlm.nih.gov/Blast.cgi BLAST Input: Select a search type BLAST Assembled Genomes Contains links to genomic BLAST pages for common organisms, and a link to a complete list of available organism genome BLAST pages Basic BLAST Contains links to BLAST forms for the traditional set of databases (e.g., nr, est, tc.). Choose the link for the search type B.I.P. etc.). Choose the link for the search type you want. For example, choose "nucleotide blast" to search a nucleotide database using a nucleotide query. Specialized BLAST Contains links to special-purpose BLAST databases and tools such as trace archives and IgBLAST
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BLAST Input: Input a QUERY sequence and select a SUBJECT database Enter a QUERY sequence Provides a place to input or upload your query sequence, and optionally select a query subrange. Choose Search Set Is where you select a database and optionally limit your search by an organism or Entrez query. The default database "Human genomic + Select “nr” database transcript", implicitly limits the search to Human. You can also select a database that is not species-specific (e.g., nr). Program selection Allows you to optimize your search for different scenarios (e.g., intra- vs. inter-species searches). The choices correspond to megablast, discontiguous megablast, and blastn for nucleotide; and blastp, PSI-BLAST and PHI-BLAST for protein.
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BLAST Input: Advanced parameters Max Target Sequences Maximum number of aligned sequences to display in results Short Queries Improve results for short queries E-value cutoff Expected number of chance matches in a random model, i.e. by chance. Default: 10 matches per query Word Size The length of the seed (short DNA/protein sequence) that initiates an alignment. atch/Mismatch Scores
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This note was uploaded on 04/26/2011 for the course MIMM 386 taught by Professor Malcolmbaines during the Spring '11 term at McGill.

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Blast and CulstalW tutorials - BLAST Input: Select a search...

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