Scoring profile-to-profile sequence alignments
نویسندگان
چکیده
منابع مشابه
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...
متن کاملFFAS03: a server for profile–profile sequence alignments
The FFAS03 server provides a web interface to the third generation of the profile-profile alignment and fold-recognition algorithm of fold and function assignment system (FFAS) [L. Rychlewski, L. Jaroszewski, W. Li and A. Godzik (2000), Protein Sci., 9, 232-241]. Profile-profile algorithms use information present in sequences of homologous proteins to amplify the patterns defining the family. A...
متن کاملProfile alignment scoring functions A comparison of scoring functions for protein sequence profile alignment
Motivation: In recent years, several methods have been proposed for aligning two protein sequence profiles, with reported improvements in alignment accuracy and homolog discrimination versus sequence-sequence methods (e.g. BLAST) and profile-sequence methods (e.g. PSIBLAST). Profile-profile alignment is also the iterated step in progressive multiple sequence alignment algorithms such as CLUSTAL...
متن کاملOptimizing the size of the sequence profiles to increase the accuracy of protein sequence alignments generated by profile-profile algorithms
MOTIVATION Profile-based protein homology detection algorithms are valuable tools in genome annotation and protein classification. By utilizing information present in the sequences of homologous proteins, profile-based methods are often able to detect extremely weak relationships between protein sequences, as evidenced by the large-scale benchmarking experiments such as CASP and LiveBench. RE...
متن کاملScoring Pairwise Genomic Sequence Alignments
The parameters by which alignments are scored can strongly affect sensitivity and specificity of alignment procedures. While appropriate parameter choices are well understood for protein alignments, much less is known for genomic DNA sequences. We describe a straightforward approach to scoring nucleotide substitutions in genomic sequence alignments, especially human-mouse comparisons. Scores ar...
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ژورنال
عنوان ژورنال: Protein Science
سال: 2004
ISSN: 0961-8368,1469-896X
DOI: 10.1110/ps.03601504