Multiple structure alignment and consensus identification for proteins
نویسندگان
چکیده
منابع مشابه
MARNA: multiple alignment and consensus structure prediction of RNAs based on sequence structure comparisons
MOTIVATION Due to the importance of considering secondary structures in aligning functional RNAs, several pairwise sequence-structure alignment methods have been developed. They use extended alignment scores that evaluate secondary structure information in addition to sequence information. However, two problems for the multiple alignment step remain. First, how to combine pairwise sequence-stru...
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Motivation: Comparing protein structures is important for understanding the relationships between sequence, structure and function. With the increasing number of experimentally determined protein structures, an automated algorithm that can perform structure alignment of many proteins is therefore highly advantageous. Results: We present a novel approach for multiple structure alignment of prote...
متن کاملMethods for multiple alignment and consensus structure prediction of RNAs implemented in MARNA.
Multiple alignments of RNAs are an essential prerequisite to further analyses such as homology modeling, motif description, or illustration of conserved or variable binding sites. Beyond the comparison of RNAs on the sequence level, structural conformations determined by basepairs have to be taken into account. Several pairwise sequence-structure alignment methods have been developed. They use ...
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Root mean square deviation (RMSD) is often used to measure the difference between structures. We show mathematically that, for multiple structure alignment, the minimum RMSD (weighted at aligned positions or unweighted) for all pairs is the same as the RMSD to the average of the structures. Thus, using RMSD implies that the average is a consensus structure. We use this property to validate and ...
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MOTIVATION Accurate gene structure annotation is a challenging computational problem in genomics. The best results are achieved with spliced alignment of full-length cDNAs or multiple expressed sequence tags (ESTs) with sufficient overlap to cover the entire gene. For most species, cDNA and EST collections are far from comprehensive. We sought to overcome this bottleneck by exploring the possib...
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ژورنال
عنوان ژورنال: BMC Bioinformatics
سال: 2010
ISSN: 1471-2105
DOI: 10.1186/1471-2105-11-71