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FASTA Herder: a web application to trim protein sequence sets

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      Abstract

      The ever increasing number of sequences in protein databases usually turns out large numbers of homologs in sequence similarity searches. While information from homology can be very useful for functional prediction based on amino acid conservation, many of these homologs usually have high levels of identity among themselves, which hinders multiple sequence alignment computation and, especially, visualization. More generally, high redundancy reduces the usability of a protein set in machine learning applications and biases statistical analyses. We developed an algorithm to identify redundant sequence homologs that can be culled producing a streamlined FASTA file. As a difference from other automatic approaches that only aggregate sequences with high identity, our method clusters near-full length homologs allowing for lower sequence identity thresholds. Our method was fully tested and implemented in a web application called FASTA Herder, publicly available at http://fh.ogic.ca/.

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      BLAST+: architecture and applications

      Background Sequence similarity searching is a very important bioinformatics task. While Basic Local Alignment Search Tool (BLAST) outperforms exact methods through its use of heuristics, the speed of the current BLAST software is suboptimal for very long queries or database sequences. There are also some shortcomings in the user-interface of the current command-line applications. Results We describe features and improvements of rewritten BLAST software and introduce new command-line applications. Long query sequences are broken into chunks for processing, in some cases leading to dramatically shorter run times. For long database sequences, it is possible to retrieve only the relevant parts of the sequence, reducing CPU time and memory usage for searches of short queries against databases of contigs or chromosomes. The program can now retrieve masking information for database sequences from the BLAST databases. A new modular software library can now access subject sequence data from arbitrary data sources. We introduce several new features, including strategy files that allow a user to save and reuse their favorite set of options. The strategy files can be uploaded to and downloaded from the NCBI BLAST web site. Conclusion The new BLAST command-line applications, compared to the current BLAST tools, demonstrate substantial speed improvements for long queries as well as chromosome length database sequences. We have also improved the user interface of the command-line applications.
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        Gapped BLAST and PSI-BLAST a new generation of protein database search programs

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          CD-HIT Suite: a web server for clustering and comparing biological sequences

          Summary: CD-HIT is a widely used program for clustering and comparing large biological sequence datasets. In order to further assist the CD-HIT users, we significantly improved this program with more functions and better accuracy, scalability and flexibility. Most importantly, we developed a new web server, CD-HIT Suite, for clustering a user-uploaded sequence dataset or comparing it to another dataset at different identity levels. Users can now interactively explore the clusters within web browsers. We also provide downloadable clusters for several public databases (NCBI NR, Swissprot and PDB) at different identity levels. Availability: Free access at http://cd-hit.org Contact: liwz@sdsc.edu Supplementary information: Supplementary data are available at Bioinformatics online.
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            Author and article information

            Affiliations
            [1 ]Ottawa Hospital Research Institute, 501 Smyth Road, Ottawa, ON K1H 8L6, Canada
            [2 ]Max Delbrük Center for Molecular Medicine, Robert-Rössle-Str. 10, 13125 Berlin, Germany
            [3 ]Department of Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada
            Author notes
            [* ]Corresponding author's e-mail address: cpereziratxeta@ 123456gmail.com
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            Journal
            SOR-LIFE
            ScienceOpen Research
            ScienceOpen
            2199-1006
            23 July 2015
            15 September 2015
            : 0 (ID: 5df5dc75-0b14-497d-804d-0075d0201d15 )
            : 0
            : 1-4
            2927:XE 10.14293/S2199-1006.1.SOR-LIFE.A67837.v2
            © 2015 Louis-Jeune et al.

            This work has been published open access under Creative Commons Attribution License CC BY 4.0 , which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Conditions, terms of use and publishing policy can be found at www.scienceopen.com .

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