Introduction to Bioinformatics

Introduction to Bioinformatics - COIN81

Assignment Two - BLAST and Sequence Alignment Tools

Genome Sequencing Tools, Using NCBI BLAST, and the NCBI Data Model

Do the 10 exercise searches using BLAST.htm . For each entry, use BLAST to arrive at the GenBank record (nucleotide or protein). Save each GenBank record in FASTA and flatfile format. I have done that for AB003468 - FASTA and flatfile formats. This may seem like a tedious activity - and it's exactly that. This is a skill that you should be able to do "with your eyes closed". Zip all 20 (or more) text files, and email the zipped archive to me. Hint: send it to yourself *first* to ensure you have zipped the entire folder.

BLAST exercises - (please see BLAST.htm) - this page will give you five nucleotide and five protein sequences to search and explore.

Standard nucleotide-nucleotide BLAST [blastn]
Standard protein-protein BLAST [blastp]
Nucleotide query - Protein db [blastx]
Protein query - Translated db [tblastn]
Nucleotide query - Translated db [tblastx]

For BLAST, I strongly recommend that you try the NCBI tutorials (BLAST Query and BLAST Tutorial and BLAST Guide) as a warm up exercise

BLAST - Basic Local Alignment Search Technique. Consisting of BLASTn, BLASTp, BLASTx, tBLASTn, tBLASTx

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