Filtering Redundancies For Sequence Similarity Search Programs

Abstract

Database scanning programs such as BLAST and FASTA are used nowadays by most biologists for the post-genomic processing of DNA or protein sequence information (in particular to retrieve the structure/function of uncharacterized proteins). Unfortunately, their results can be polluted by identical alignments (called redundancies) coming from the same protein or DNA sequences present in different entries of the database. This makes the efficient use of the listed alignments difficult. Pretreatment of databases has been proposed to suppress strictly identical entries. However, there still remain many identical alignments since redundancies may occur locally for entries corresponding to various fragments of the same sequence or for entries corresponding to very homologous sequences but differing at the level of a few residues such as ortholog proteins. In the present work, we show that redundant alignments can be indeed numerous even when working with a pretreated non-redundant data bank, going as high as 60% of the output results according to the query and the bank. Therefore the accuracy and the efficiency of the post-genomic work will be greatly increased if these redundancies are removed. To solve this up to now unaddressed problem, we have developed an algorithm that allows for the efficient and safe suppression of all the redundancies with no loss of information. This algorithm is based on various filtering steps that we describe here in the context of the Automat similarity search program, and such an algorithm should also be added to the other similarity search programs (BLAST, FASTA, etc...).

RPBS: a web resource for structural bioinformatics

“…AUTOMAT has been the first software program to introduce histograms presenting the frequencies in the database of all the words of the query larger than w and to delete automatically redundant alignments originating from different sequences in the output listing (10,11). AUTOMAT and BLAST lead to coherent results for protein sequences in comparable computer time, but for nucleic acids AUTOMAT allows triggers w shorter (5 characters by default) than BLAST (words of 11 characters), thus leading to more sensitivity than BLAST.…”