note - FIZ Karlsruhe

Introduction to similarity searching
GETSIM alignments for nucleic acid sequences
Similarity in GETSIM alignments is represented by line of dots or blanks placed between two
lines representing the query sequence (upper line) and the hit subject sequence (lower line). Two
dots mark a full match between two nucleic acid sequence letters and blanks show non-matching
letters. One dot represents a “family” similarity match between Uracil (U) and Thymine (T). Gaps
represented by an underscore, may be introduced into the query or the subject sequence for a
better alignment of both sequences. Inclusion of gaps in this way reduces the similarity score.
Example
ALIGN Smith-Waterman score: 57
33 na overlap starting at 546
aggagugguaggucuuacgaugccagcuguaau ← Query
:: : . .: . .: : ::::::.: ::.
Agtattcatatttactaacaagccagctggaat ← Answer
GETSIM alignments for amino acid sequences
Similarity in GETSIM alignments of amino acid sequences is represented by line of dots or blanks
placed between two lines representing the query sequence (upper line) and the hit subject sequence
(lower line). Two dots mark a full match between two amino acid letters and one dot represents
an amino acid family match. Blanks show non-matching letters. Gaps represented by an
underscore, may be introduced into the query or the subject sequence for a better alignment of
both sequences. Inclusion of gaps in this way reduces the similarity score.
Example
ALIGN Smith-Waterman score: 80
49 aa overlap starting at 569
vge_gaiplsigyatllhmdqgvalgrvlpmvmlggltaiiisgclnql ← Query
::: :: :: . :: : .::: .. .::.... ....: .:
vgeygasplclpyap__pegqpaalgftvalvmmnsfcflvvagayikl ← Answer
Helpful
HINT
GETSIM is slower than BLAST, so using GETSIM in BATCH mode is
recommended. In addition, BATCH query limits are higher. See page 79.
GENESEQ on STN (DGENE) Workshop Manual | Page 19