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ProfileGrids as a new visual representation of large multiple sequence alignments: a case study of the RecA protein family

Alberto I Roca*, Albert E Almada and Aaron C Abajian

BMC Bioinformatics 2008, 9:554  doi:10.1186/1471-2105-9-554

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JProfileGrid version 2.0 released

Alberto Roca   (2013-03-10 13:36)  ProfileGrid.org

New JProfileGrid v2.0 can visualize alignments of >100,000 sequences. New features have also been introduced such as sorting and searching the menu list of sequence names for finding a specific homolog to serve as the reference sequence for the ProfileGrid. The new "overview" modes enable the user to visualize the entire MSA within one window as either a ProfileGrid or a stacked sequence. A ProfileGrid can now be exported as a PNG image file. The detailed ProfileGrid window with the character counts has a new second pane that facilitates simultaneous viewing of different parts of the MSA. To focus on rare residues, the "highlight" functionality now identifies residues that occur greater or less than a user-defined threshold of residue frequency. We introduced data sampling to accelerate similarity plot calculations. Regular expression functionality has also been implemented to find sequences with particular names or amino acid patterns. Finally, JProfileGrid can import simple sequence annotations from flat file spreadsheet databases for meta data filtering to reduce large MSAs to subsets of interest. We demonstrate the latter two features on an alignment of 11,900 hemagglutinin protein sequences.

REFERENCE:
Alberto I Roca, Aaron C Abajian, David J Vigerust
ProfileGrids solve the large alignment visualization problem: influenza hemagglutinin example.
F1000Research 2:2 (2013)
http://f1000research.com/articles/2-2/

Competing interests

We have developed the software but have no competing interests.

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