Software tools for analyzing pairwise alignments of long sequences
نویسندگان
چکیده
منابع مشابه
Software tools for analyzing pairwise alignments of long sequences.
Pairwise comparison of long stretches of genomic DNA sequence can identify regions conserved across species, which often indicate functional significance. However, the novel insights frequently must be windowed from a flood of information; for instance, running an alignment program on two 50-kilobase sequences might yield over a hundred pages of alignments. Direct inspection of such a volume of...
متن کاملPost-processing long pairwise alignments
MOTIVATION The local alignment problem for two sequences requires determining similar regions, one from each sequence, and aligning those regions. For alignments computed by dynamic programming, current approaches for selecting similar regions may have potential flaws. For instance, the criterion of Smith and Waterman can lead to inclusion of an arbitrarily poor internal segment. Other approach...
متن کاملDetecting overlapping coding sequences with pairwise alignments
MOTIVATION Overlapping gene coding sequences (CDSs) are particularly common in viruses but also occur in more complex genomes. Detecting such genes with conventional gene-finding algorithms can be difficult for several reasons. If an overlapping CDS is on the same read-strand as a known CDS, then there may not be a distinct promoter or mRNA. Furthermore, the constraints imposed by double-coding...
متن کاملMultiple Pairwise Sequences Alignments with Needleman-Wunsch Algorithm on GPU
Pairwise sequence alignment is the method to find the best matching piece for two sequences. It can be either local which return the most similar subsequence or global which return the alignment of whole sequence. Nowadays, the number of genetic sequences increases exponentially so that it becomes a challenge to analyze and understand those data. The cutting-edge parallel architectures provide ...
متن کاملStochastic pairwise alignments
MOTIVATION The level of sequence conservation between related nucleic acids or proteins often varies considerably along the sequence. Both regions with high variability (mutational hot-spots) and regions of almost perfect sequence identity may occur in the same pair of molecules. The reliability of an alignment therefore strongly depends on the level of local sequence similarity. Especially in ...
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ژورنال
عنوان ژورنال: Nucleic Acids Research
سال: 1991
ISSN: 0305-1048,1362-4962
DOI: 10.1093/nar/19.17.4663