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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.
The fourth is a great example of how interactive graphical tools enable a worker involved in sequence analysis to conveniently execute a variety if different computational tools to explore an alignment's phylogenetic implications; or, to predict the structure and functional properties of a specific sequence, e.g., comparative modelling.
In the field of translation studies a bitext is a merged document composed of both source- and target-language versions of a given text. Bitexts are generated by a piece of software called an alignment tool, or a bitext tool, which automatically aligns the original and translated versions of the same text. The tool generally matches these two ...
The alignment tools of the time were not capable of performing these operations in a manner that would allow a regular update of the human genome assembly. Compared to pre-existing tools, BLAT was ~500 times faster with performing mRNA / DNA alignments and ~50 times faster with protein /protein alignments.
Uses adaptative seeds and copes more efficiently with repeat-rich sequences (e.g. genomes). For example: it can align reads to genomes without repeat-masking, without becoming overwhelmed by repetitive hits. Yes Yes Yes Yes Free, GPL [46] 2011 MAQ Ungapped alignment that takes into account quality scores for each base. Free, GPL: mrFAST, mrsFAST
Additionally, flush-right alignment is used to set off special text in English, such as attributions to authors of quotes printed in books and magazines, or text associated with an image to its right. Flush right is often used when formatting tables of data. It is used to align text to the right margin; in this case, the left ends will be unequal.
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Alignment of 27 avian influenza hemagglutinin protein sequences colored by residue conservation (top) and residue properties (bottom) 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.