ddbRNA: detection of conserved secondary structures in multiple alignments
نویسندگان
چکیده
منابع مشابه
ddbRNA: detection of conserved secondary structures in multiple alignments
MOTIVATION Structured non-coding RNAs (ncRNAs) have a very important functional role in the cell. No distinctive general features common to all ncRNA have yet been discovered. This makes it difficult to design computational tools able to detect novel ncRNAs in the genomic sequence. RESULTS We devised an algorithm able to detect conserved secondary structures in both pairwise and multiple DNA ...
متن کاملDetection of unrelated proteins in sequences multiple alignments by using predicted secondary structures
MOTIVATION Multiple sequence alignments are essential tools for establishing the homology relations between proteins. Essential amino acids for the function and/or the structure are generally conserved, thus providing key arguments to help in protein characterization. However for distant proteins, it is more difficult to establish, in a reliable way, the homology relations that may exist betwee...
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Recently, non-coding RNAs (ncRNAs) have been discovered with novel functions, and it has been appreciated that there is pervasive transcription of genomes. Moreover, many novel ncRNAs are not conserved on the primary sequence level. Therefore, de novo computational ncRNA detection that is accurate and efficient is desirable. The purpose of this study is to develop a ncRNA detection method based...
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BACKGROUND Recent evidence suggests that the number and variety of functional RNAs (ncRNAs as well as cis-acting RNA elements within mRNAs) is much higher than previously thought; thus, the ability to computationally predict and analyze RNAs has taken on new importance. We have computationally studied the secondary structures in an alignment of six Aspergillus genomes. Little is known about the...
متن کاملNASP: a parallel program for identifying evolutionarily conserved nucleic acid secondary structures from nucleotide sequence alignments
SUMMARY Many natural nucleic acid sequences have evolutionarily conserved secondary structures with diverse biological functions. A reliable computational tool for identifying such structures would be very useful in guiding experimental analyses of their biological functions. NASP (Nucleic Acid Structure Predictor) is a program that takes into account thermodynamic stability, Boltzmann base pai...
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ژورنال
عنوان ژورنال: Bioinformatics
سال: 2003
ISSN: 1367-4803,1460-2059
DOI: 10.1093/bioinformatics/btg229