Open Access Methodology article

Combination of measures distinguishes pre-miRNAs from other stem-loops in the genome of the newly sequenced Anopheles darlingi

Nuno D Mendes123*, Ana T Freitas2, Ana T Vasconcelos4 and Marie-France Sagot13

Author Affiliations

1 Équipe BAOBAB, Laboratoire de Biométrie et Biologie Évolutive (UMR 5558); CNRS; Univ. Lyon 1, 43 bd du 11 nov 1918, 69622, Villeurbanne Cedex, France

2 IST/INESC-ID, 9 Rua Alves Redol, 1000-029 Lisbon, Portugal

3 BAMBOO Team, INRIA Rhone-Alpes, 655 avenue de l'Europe, 38330 Montbonnot Saint-Martin, France

4 Bioinformatics Laboratory, National Laboratory of Scientific Computation (LNCC), Avenida Getúlio Vargas, 333, Petrópolis, Brazil

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BMC Genomics 2010, 11:529  doi:10.1186/1471-2164-11-529

Published: 29 September 2010

Additional files

Additional file 1:

Extractor. Source code for C program which identifies candidate regions potentially containing stem-loops in a dataset of interest. Source code for PERL programs which identify and filter stem-loops within the extracted candidate regions.

Format: GZ Size: 15KB Download file

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Additional file 2:

Loading information onto database. Source code for PERL programs that load precursor information onto the database.

Format: GZ Size: 5KB Download file

Open Data

Additional file 3:

Computing evaluation measures. Source code for PERL programs that compute the evaluation measures and calculate the composite score.

Format: GZ Size: 5KB Download file

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Additional file 4:

Common PERL modules. PERL Modules shared across all PERL programs.

Format: GZ Size: 13KB Download file

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Additional file 5:

Generating graphs. PERL programs which generate R scripts that calculate and draw graphs.

Format: GZ Size: 5KB Download file

Open Data

Additional file 6:

Supplementary Materials. Detailed presentation of the candidate enumeration procedure. Table showing the homologs to pre-miRNAs of A. gambiae identified amongst the precursor candidates of A. darlingi. Table showing the alignments of mature miRNAs from A. gambiae with precursor homologs identified amongst precursor candidates from A. darlingi.

Format: PDF Size: 150KB Download file

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