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Permanent link (DOI): https://doi.org/10.7939/R3599Z555

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A cross-species alignment tool (CAT) Open Access

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Author or creator
Li, H.
Guan, L.
Liu, T.
Guo, Y.
Zheng, W.M.
Wong, G.K.
Wang, J.
Additional contributors
Subject/Keyword
programs
search
genomic DNA
databases
sequences
annotation
blast
Type of item
Journal Article (Published)
Language
English
Place
Time
Description
Background The main two sorts of automatic gene annotation frameworks are ab initio and alignment-based, the latter splitting into two sub-groups. The first group is used for intra-species alignments, among which are successful ones with high specificity and speed. The other group contains more sensitive methods which are usually applied in aligning inter-species sequences. Results Here we present a new algorithm called CAT (for Cross-species Alignment Tool). It is designed to align mRNA sequences to mammalian-sized genomes. CAT is implemented using C scripts and is freely available on the web at  http://xat.sourceforge.net/
webcite. Conclusions Examined from different angles, CAT outperforms other extant alignment tools. Tested against all available mouse-human and zebrafish-human orthologs, we demonstrate that CAT combines the specificity and speed of the best intra-species algorithms, like BLAT and sim4, with the sensitivity of the best inter-species tools, like GeneWise.

Date created
2007
DOI
doi:10.7939/R3599Z555
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© 2007 Li et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Citation for previous publication
H Li, L Guan, T Liu, Y Guo, WM Zheng, GK Wong, J Wang. "A cross-species alignment tool (CAT)." BMC Bioinformatics 8 (2007): 349
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