Optimization of ribosomal RNA profile alignments

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چکیده

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منابع مشابه

Optimization of ribosomal RNA profile alignments

MOTIVATION Large alignments of ribosomal RNA sequences are maintained at various sites. New sequences are added to these alignments using a combination of manual and automatic methods. We examine the use of profile alignment methods for rRNA alignment and try to optimize the choice of parameters and sequence weights. RESULTS Using a large alignment of eukaryotic SSU rRNA sequences as a test c...

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Empirical estimation of the reliability of ribosomal RNA alignments

MOTIVATION The automatic alignment of rRNA sequences can reproduce manual expert alignments with high, but not perfect, fidelity. We examine the use of empirical methods for the identification of regions of an alignment of a new sequence with an existing large alignment which can confidently be predicted to be correctly aligned. RESULTS We show how to use a simple jack-knife procedure to deri...

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Semiautomated improvement of RNA alignments.

We have developed a semiautomated RNA sequence editor (SARSE) that integrates tools for analyzing RNA alignments. The editor highlights different properties of the alignment by color, and its integrated analysis tools prevent the introduction of errors when doing alignment editing. SARSE readily connects to external tools to provide a flexible semiautomatic editing environment. A new method, Pc...

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Consensus sequences improve PSI-BLAST through mimicking profile–profile alignments

Sequence alignments may be the most fundamental computational resource for molecular biology. The best methods that identify sequence relatedness through profile-profile comparisons are much slower and more complex than sequence-sequence and sequence-profile comparisons such as, respectively, BLAST and PSI-BLAST. Families of related genes and gene products (proteins) can be represented by conse...

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Improving Profile-Profile Alignments via Log Average Scoring

Alignments of frequency profiles against frequency profiles have a wide scope of applications in currently used bioinformatic analysis tools ranging from multiple alignment methods based on the progressive alignment approach to detecting of structural similarities based on remote sequence homology. We present the new log average scoring approach to calculating the score to be used with alignmen...

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ژورنال

عنوان ژورنال: Bioinformatics

سال: 1998

ISSN: 1367-4803,1460-2059

DOI: 10.1093/bioinformatics/14.4.332