LASSAP, a LArge Scale Sequence compArison Package

Motivation: This paper presents LASSAP, a new software package for sequence comparison. LASSAP is a programmable, high-performance system designed to raise current limitations of sequence comparison programs in order to fit the needs of large-scale analysis. LASSAP provides an API (Application Progr...

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Bibliographic Details
Published in:Bioinformatics Vol. 13; no. 2; pp. 137 - 143
Main Authors: Glemet, E, Codani, J.J
Format: Journal Article
Language:English
Published: Washington, DC Oxford University Press 01.04.1997
Oxford
Subjects:
algorithm integration
Algorithms
Amino Acid Sequence
amino acid sequences
Base Sequence
Biological and medical sciences
comparisons
computer analysis
computer software
Databases, Factual
Evaluation Studies as Topic
Fundamental and applied biological sciences. Psychology
General aspects
genetics
Mathematics in biology. Statistical analysis. Models. Metrology. Data processing in biology (general aspects)
methods
Molecular Sequence Data
Nucleic Acids
Nucleic Acids - genetics
nucleotide sequences
Proteins
Proteins - genetics
Sequence Alignment
Sequence Alignment - methods
Sequence Alignment - statistics & numerical data
Software
statistics & numerical data
Proteins
Nucleotide sequence
Computerized processing
Database
Software
Method
Algorithm
Nucleic acid
Comparative study
Aminoacid sequence
ISSN:0266-7061, 1367-4803, 1460-2059
Online Access:Get full text
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Summary:Motivation: This paper presents LASSAP, a new software package for sequence comparison. LASSAP is a programmable, high-performance system designed to raise current limitations of sequence comparison programs in order to fit the needs of large-scale analysis. LASSAP provides an API (Application Programming Interface) allowing the integration of any generic pairwise-based algorithm. Results: Whatever pairwise algorithm is used in LASSAP, it shares with all other algorithms numerous enhancements such as: (i) intra- and inter-databank comparisons; (ii) computational requests (selections and computations are achieved on the fly); (iii) frame translations on queries and databanks; (iv) structured results allowing easy and powerful post-analysis; (v) performance improvements by parallelization and the driving of specialized hardware. LASSAP currently implements all major sequence comparison algorithms (Fasta, Blast, Smith/Waterman), and other string matching and pattern matching algorithms. LASSAP is both an integrated software for end-users and a framework allowing the integration and the combination of new algorithms. LASSAP is used in different projects such as the building of PRODOM, the exhaustive comparison of yeast sequences, and the subfragments matching problem of TREMBL.
Bibliography:1To whom correspondence should be addressed
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ISSN:0266-7061
1367-4803
1460-2059
DOI:10.1093/bioinformatics/13.2.137