Title

Authors

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

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 NCBI’s 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.