Naslov
Trade-offs in query and target indexing for the selection of candidates in protein homology searches

Autori
Ristov, Strahil ; Vaser, Robert ; Šikić, Mile

Vrsta, podvrsta i kategorija rada
Radovi u zbornicima skupova, cjeloviti rad (in extenso), znanstveni

Izvornik
Proceedings of The Prague Stringology Conference 2017 / Jan Holub and Jan Ždarek - Prag : Czech technical university in Prague, 2017, 118-125

ISBN
978-80-01-06193-0

Skup
The Prague Stringology Conference

Mjesto i datum
Prag, Češka Republika, 28.08.2017. - 30.08.2017

Vrsta sudjelovanja
Predavanje

Vrsta recenzije
Međunarodna recenzija

Ključne riječi
protein sequence homology ; string index ; SWORD ; Hamming distance vector ; diagonal counting

Sažetak
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.

Izvorni jezik
Engleski

Znanstvena područja
Računarstvo

POVEZANOST RADA