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Title

CEPiNS: Conserved Exon Prediction in Novel Species

 

Authors

Shihab Hasan1, 2 & Christopher W Wheat2, 3, 4

 

Affiliation

1Bioinformatics, Department of Information Technology, 20014, University of Turku, Finland; 2Department of Biological and Environmental Sciences, PL 65, Viikinkaari 1, 00014 University of Helsinki, Finland; 3Centre for Ecology and Conservation, School of Biosciences, University of Exeter, Cornwall Campus, Penryn, Cornwall TR10 9EZ, United Kingdom; 4Department of Zoology, Stockholm University, SE-106 91 Stockholm, Sweden.

 

Email

shihab.hasan@utu.fi; *Corresponding author

 

Article Type

Software

 

Date

Received January 17, 2013; Accepted January 29, 2013; Published February 21, 2013

 

Abstract

Exon structure is relatively well conserved among orthologs in several large clades of species (e.g. Mammalia, Diptera, Lepidoptera) across evolutionary distances of up to 80 million years. Thus, it should be straightforward to predict the exon structures in novel species based upon the known exon structures of species that have had their genomes sequenced and well assembled. Being able to predict the exon boundaries in the genes of novel species is important given the quickly growing numbers of transcriptome sequencing projects. CEPiNS is a new pipeline for mining exon boundaries of predicted gene sets from model species and then using this information to identify the exon boundaries in a novel species through codon based alignment. The pipeline uses the freeware SPIDEY, an exon boundary prediction tool, and BLAST (BLASTN, BLASTP, TBLASTX), both of which are part of NCBIís toolkit. CEPiNS provides an important tool to analyze the transcriptome of novel species.

 

Availability

http://www.cepins.org

 

Keywords

Exon prediction, Gene structure, Model species, Novel species, Transcriptomics, Evolutionary and Comparative genomics, Bioinformatics Software.

 

Citation

Hasan & Wheat, Bioinformation 9(4): 210-211 (2013)

 

Edited by

P Kangueane

 

ISSN

0973-2063

 

Publisher

Biomedical Informatics

 

License

This is an Open Access article which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. This is distributed under the terms of the Creative Commons Attribution License.