Bioinformatics for DNA Sequence Analysis.pdf - Index of

Similarity Searching Using BLAST 13Fig. 1.6. Organism selection when searching a multi-organism database.2.7.1. Max TargetSequencesThe maximum target sequences parameter allows you to select thenumber of sequences you would like displayed in your results.Lower numbers do not reduce the search time, but do reducethe time to send the results back. This is generally only an issueover a slow connection.2.7.2. Short Queries When using short queries (of length 30 or less), the parametersmust be adjusted or you will not receive statistically significantresults. Checking the ‘‘short queries’’ box automatically adjusts theparameters to return valid responses for a short query sequence.2.7.3. Expect Threshold The expect threshold limits the results displayed to those with anE-value lower than it. This value corresponds to the number ofsequence matches that are expected to be found merely by chance.2.7.4. Word Size The word size, W, as discussed earlier determines the length of thewords and neighboring words used as initial search queries.Increasing the word size generally results in fewer extension initializations,increasing the speed of the BLAST search but decreasingits sensitivity.2.7.5. Scoring Parameters The scoring parameters of a nucleotide search are the matchand mismatch scores and gap costs. In protein searches, thematch and mismatch scores are indicated by a scoring matrix(see Section 2.3). A limited set of suggested match and mismatchscores are available from the dropdown menu on NCBI’s BLASTsearch form. Increasing the ratio in the following fashion (match,mismatch): (1,–1) ! (4,–5) ! (2,–3) ! (1,–2) ! (1,–3) ! (1,–4)prevents mismatched nucleotides from aligning, increasing the