A novel approach to remote homology detection: jumping alignments

Spang R, Rehmsmeier M, Stoye J (2002)
Journal of Computational Biology 9(5): 747-760.

Zeitschriftenaufsatz | Veröffentlicht | Englisch
 
Download
OA
Autor/in
Abstract / Bemerkung
We describe a new algorithm for protein classification and the detection of remote homologs. The rationale is to exploit both vertical and horizontal information of a multiple alignment in a well-balanced manner. This is in contrast to established methods such as profiles and profile hidden Markov models which focus on vertical information as they model the columns of the alignment independently and to family pairwise search which focuses on horizontal information as it treats given sequences separately. In our setting, we want to select from a given database of "candidate sequences" those proteins that belong to a given superfamily. In order to do so, each candidate sequence is separately tested against a multiple alignment of the known members of the superfamily by means of a new jumping alignment algorithm. This algorithm is an extension of the Smith-Waterman algorithm and computes a local alignment of a single sequence and a multiple alignment. In contrast to traditional methods, however, this alignment is not based on a summary of the individual columns of the multiple alignment. Rather, the candidate sequence is at each position aligned to one sequence of the multiple alignment, called the "reference sequence". In addition, the reference sequence may change within the alignment, while each such jump is penalized. To evaluate the discriminative quality of the jumping alignment algorithm, we compare it to profiles, profile hidden Markov models, and family pairwise search on a subset of the SCOP database of protein domains. The discriminative quality is assessed by median false positive counts (med-FP-counts). For moderate med-FP-counts, the number of successful searches with our method is considerably higher than with the competing methods.
Stichworte
Homology detection; Jumping alignments; Protein classification; Sequence analysis
Erscheinungsjahr
2002
Zeitschriftentitel
Journal of Computational Biology
Band
9
Ausgabe
5
Seite(n)
747-760
ISSN
1066-5277
eISSN
1557-8666
Page URI
https://pub.uni-bielefeld.de/record/1773578

Zitieren

Spang R, Rehmsmeier M, Stoye J. A novel approach to remote homology detection: jumping alignments. Journal of Computational Biology. 2002;9(5):747-760.
Spang, R., Rehmsmeier, M., & Stoye, J. (2002). A novel approach to remote homology detection: jumping alignments. Journal of Computational Biology, 9(5), 747-760. doi:10.1089/106652702761034172
Spang, R., Rehmsmeier, M., and Stoye, J. (2002). A novel approach to remote homology detection: jumping alignments. Journal of Computational Biology 9, 747-760.
Spang, R., Rehmsmeier, M., & Stoye, J., 2002. A novel approach to remote homology detection: jumping alignments. Journal of Computational Biology, 9(5), p 747-760.
R. Spang, M. Rehmsmeier, and J. Stoye, “A novel approach to remote homology detection: jumping alignments”, Journal of Computational Biology, vol. 9, 2002, pp. 747-760.
Spang, R., Rehmsmeier, M., Stoye, J.: A novel approach to remote homology detection: jumping alignments. Journal of Computational Biology. 9, 747-760 (2002).
Spang, Rainer, Rehmsmeier, Marc, and Stoye, Jens. “A novel approach to remote homology detection: jumping alignments”. Journal of Computational Biology 9.5 (2002): 747-760.
Alle Dateien verfügbar unter der/den folgenden Lizenz(en):
Copyright Statement:
This Item is protected by copyright and/or related rights. [...]
Volltext(e)
Access Level
OA Open Access
Zuletzt Hochgeladen
2019-09-06T08:48:08Z
MD5 Prüfsumme
d74c8f1ce5f4359744115523b4715a1d

Export

Markieren/ Markierung löschen
Markierte Publikationen

Open Data PUB

Web of Science

Dieser Datensatz im Web of Science®

Quellen

PMID: 12487762
PubMed | Europe PMC

Suchen in

Google Scholar