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Campagna, D - Albiero, A - Bilardi, A - Caniato, E - Forcato, C - Manavski, S - Vitulo, N - Valle, G (2009) PASS: a program to align short sequences. [Articolo di periodico (a stampa)]

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Abstract (inglese)

SUMMARY: Standard DNA alignment programs are inadequate to manage the data produced by new generation DNA sequencers. To answer this problem, we developed PASS with the objective of improving execution time and sensitivity when compared with other available programs. PASS performs fast gapped and ungapped alignments of short DNA sequences onto a reference DNA, typically a genomic sequence. It is designed to handle a huge amount of reads such as those generated by Solexa, SOLiD or 454 technologies. The algorithm is based on a data structure that holds in RAM the index of the genomic positions of 'seed' words (typically 11 and 12 bases) as well as an index of the precomputed scores of short words (typically seven and eight bases) aligned against each other. After building the genomic index, the program scans every query sequence performing three steps: (1) it finds matching seed words in the genome; (2) for every match checks the precomputed alignment of the short flanking regions; (3) if passes step 2, then it performs an exact dynamic alignment of a narrow region around the match. The performance of the program is very striking both for sensitivity and speed. For instance, gap alignment is achieved hundreds of times faster than BLAST and several times faster than SOAP, especially when gaps are allowed. Furthermore, PASS has a higher sensitivity when compared with the other available programs. Availability and implementation: Source code and binaries are freely available for download at http://pass.cribi.unipd.it, implemented in C++and supported on Linux and Windows.


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Tipo di EPrint:Articolo di periodico (a stampa)
Anno di Pubblicazione:01 Aprile 2009
Settori scientifico-disciplinari MIUR:Area 05 - Scienze biologiche > BIO/11 Biologia molecolare
Area 01 - Scienze matematiche e informatiche > INF/01 Informatica
Area 05 - Scienze biologiche > BIO/18 Genetica
Struttura di riferimento:Centri > Centro di ricerca Interdipartimentale Biotecnologie Innovative (CRIBI)
Codice ID:2048
Depositato il:03 Giu 2009 09:00
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Le url contenute in alcuni riferimenti sono raggiungibili cliccando sul link alla fine della citazione (Vai!) e tramite Google (Ricerca con Google). Il risultato dipende dalla formattazione della citazione.

Altschul,SF, Gish W, Miller W, Myers EW, Lipman DJ. (1990) Basic local alignment search tool. J Mol Biol. 215, 403-410. Cerca con Google

Baeza-Yates,R., Navarro,G (1996). A faster algorithm for approximate string matching. In Combinatorial Pattern Matching, Irvine,CA,LNCS1075,Jun96, 1-23. Cerca con Google

Church, G. (2005). The Personal Genome Project. Mol. Syst. Biol. 1, 0030. Cerca con Google

Jiang,H., Wong,W.H. (2008). SeqMap: mapping massive amount of oligonucleotides to the genome. Bioinformatics. 24, 2395-2396. Cerca con Google

Kent,WJ. (2002) BLAT-the BLAST-like alignment tool. Genome Res. 12, 656- 664. Cerca con Google

Li,H., Ruan,J., Durbin,R. (2008a). Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Res. 18, 1851-1858. Cerca con Google

Li,R., Li,Y., Kristiansen,K., Wang,J. (2008b) SOAP: short oligonucleotide alignment program. Bioinformatics. 24, 713-714. Cerca con Google

Manavski,S.A., Valle,G. (2008). CUDA compatible GPU cards as efficient hardware accelerators for Smith-Waterman sequence alignment. BMC Bioinformatics, 9, Suppl 2:S10. Cerca con Google

Needleman,S.B, Wunsch,C.D. (1970). A general method applicable to the search for similarities in the amino acid sequence of two proteins. J Mol Biol. 48, 443- 453. Cerca con Google

Ning,Z, Cox,A.J., Mullikin,J.C. (2001) SSAHA: a fast search method for large DNA databases. Genome Res. 11, 1725-1729. Cerca con Google

Pearson,WR., Lipman,D.J. (1988) Improved tools for biological sequence comparison. PNAS 85, 2444-2448. Cerca con Google

Prüfer,K., Stenzel,U., Dannemann,M., Green,R.E., Lachmann,M. And Kelso,J.(2008). PatMaN: rapid alignment of short sequences to large databases . Bioinformatics 24, 1530-1532. Cerca con Google

Smith,A.D., Xuan,Z. and Zhang,M.Q.(2008). Using quality scores and longer reads improves accuracy of Solexa read mapping. BMC Bioinformatics, 9:128. Cerca con Google

Lin,H., Zhang,Z., Zhang,M.Q., Ma,B., Li,M. (2008). ZOOM: Zillion of Oligos Mapped. Bioinformatics, 24, 2431-2437. Cerca con Google

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