Search results
Results from the WOW.Com Content Network
Microsoft Word - Annotated Multiple Sequence Alignment.docx: Author: Andrea Smolinski: Software used: Microsoft Word: Conversion program: Mac OS X 10.5.8 Quartz PDFContext: Encrypted: no: Version of PDF format: 1.3: Page size: 612 x 792 pts (letter)
Multiple sequence alignment (MSA) is the process or the result of sequence alignment of three or more biological sequences, generally protein, DNA, or RNA. These alignments are used to infer evolutionary relationships via phylogenetic analysis and can highlight homologous features between sequences.
Stockholm format is a multiple sequence alignment format used by Pfam, Rfam and Dfam, to disseminate protein, RNA and DNA sequence alignments. [1] [2] [3] The alignment editors Ralee, [4] Belvu and Jalview support Stockholm format as do the probabilistic database search tools, Infernal and HMMER, and the phylogenetic analysis tool Xrate.
Multiple sequence alignment is an extension of pairwise alignment to incorporate more than two sequences at a time. Multiple alignment methods try to align all of the sequences in a given query set. Multiple alignments are often used in identifying conserved sequence regions across a group of sequences hypothesized to be evolutionarily related.
The SAM format consists of a header and an alignment section. [1] The binary equivalent of a SAM file is a Binary Alignment Map (BAM) file, which stores the same data in a compressed binary representation. [4] SAM files can be analysed and edited with the software SAMtools. [1] The header section must be prior to the alignment section if it is ...
Circular Multiple Sequence Alignment where the start and end of protein sequences can vary to find better matches. Circular multiple sequence alignment – A common assumption of multiple sequence alignment techniques is that the left- and right-most positions of the input sequences are relevant to the alignment. However, the position where a ...
The rest of this article is focused on only multiple global alignments of homologous proteins. The first two are a natural consequence of most representations of alignments and their annotation being human-unreadable and best portrayed in the familiar sequence row and alignment column format, of which examples are widespread in the literature.
The multiple sequence alignment problem is generally based on pairwise sequence alignment and currently, for a pairwise sequence alignment problem, biologists can use a dynamic programming approach to obtain its optimal solution. However, the multiple sequence alignment problem is still one of the more challenging problems in bioinformatics.