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Biological Relevance

Find evolutionary related sequences for phylogenetic analysis, by using BLAST to help identify similar sequences then use manual identification of the hits to select sequences for multiple sequence alignment.

Primary persona: Jane

Jane is a first year bioinformatics masters student, female, 28 years old. worked for a health research institute for 4 years. Prior knowledge of computers but not bioinformatics. Attended 6 months worth of introductory bioinformatics courses.

Secondary persona: Professor Bob

Professor Bob is the project leader. 38 years old and has been involved in sequencing projects for the past ten years. Has knowledge of the advanced BLAST settings.

Scenario 1.

Start with a sequence in Genbank format displayed in a web browser. Use the sequence as input to the BLAST similarity search of the "nr" database. Select the hits with an E-value better than 1e-70 and export those sequence records in FASTA format, for use by CLUSTALW on Jane's machine.

Scenario 2.

Start with a sequence record in FASTA format in the file "abc.fasta" on Jane's machine and search the "kinase" database. From the graphical overview of the BLAST results Jane sees that one hit aligns to a different part of the target than the others. She's curious and wants to find out more information about that outlier.

Scenario 3.

Jane got an urgent SMS from Professor Bob to find more information about NBN:12345, a sequence record in the local NBN database. Email him the results of a BLAST search against the "local" database.

System Requirements

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