Trade-offs in query and target indexing for the selection of candidates in protein homology searches (CROSBI ID 651522)
Prilog sa skupa u zborniku | izvorni znanstveni rad | međunarodna recenzija
Podaci o odgovornosti
Ristov, Strahil ; Vaser, Robert ; Šikić, Mile
engleski
Trade-offs in query and target indexing for the selection of candidates in protein homology searches
We compare two recent similar and complementary indexing methods for fast seed discovery [10, 12]. Both methods are based on the principle of counting matches on a diagonal with a goal to find the value and/or position of the best match between two sequences under Hamming distance on alphabet of k-mers, where k can equal 1. The matching k-mers in two sequences are found by scanning one sequence and using the index of the other. Indexing the shorter of the two sequences is easier to perform on-line ; however, if the index is constructed off-line on the longer sequence, the number of comparison operation is potentially much smaller. We present the analysis of this effect for different real data sequence lengths in the context of protein search.
protein sequence homology ; string index ; SWORD ; Hamming distance vector ; diagonal counting
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Podaci o prilogu
118-125.
2017.
objavljeno
Podaci o matičnoj publikaciji
Proceedings of The Prague Stringology Conference 2017
Jan Holub and Jan Ždarek
Prag: Czech technical university in Prague
978-80-01-06193-0
Podaci o skupu
The Prague Stringology Conference
predavanje
28.08.2017-30.08.2017
Prag, Češka Republika