Dataset Information

Improved prediction of conopeptide superfamilies with ConoDictor 2.0.

ABSTRACT:

Motivation

Cone snails are among the richest sources of natural peptides with promising pharmacological and therapeutic applications. With the reduced costs of RNAseq, scientists now heavily rely on venom gland transcriptomes for the mining of novel bioactive conopeptides, but the bioinformatic analyses often hamper the discovery process.

Results

Here, we present ConoDictor 2.0 as a standalone and user-friendly command-line program. We have updated the program originally published as a web server 10 years ago using novel and updated tools and algorithms and improved our classification models with new and higher quality sequences. ConoDictor 2.0 is now more accurate, faster, multiplatform and able to deal with a whole cone snail venom gland transcriptome (raw reads or contigs) in a very short time. The new version of Conodictor also improves the identification and subsequent classification for entirely novel or relatively distant conopeptides. We conducted various tests on known conopeptides from public databases and on the published venom duct transcriptome of Conus geographus, and compared previous results with the output of ConoDictor 2.0, ConoSorter and BLAST. Overall, ConoDictor 2.0 is 4 to 8 times faster for the analysis of a whole transcriptome on a single core computer and performed better at predicting gene superfamily.

Availability and implementation

ConoDictor 2.0 is available as a python 3 git folder at https://github.com/koualab/conodictor.

Supplementary information

Supplementary data are available at Bioinformatics Advances online.

SUBMITTER: Koua D

PROVIDER: S-EPMC9710579 | biostudies-literature | 2021

REPOSITORIES: biostudies-literature

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Publications

Improved prediction of conopeptide superfamilies with ConoDictor 2.0.

Koua Dominique D Ebou Anicet A Dutertre Sébastien S

Bioinformatics advances 20210617 1

<h4>Motivation</h4>Cone snails are among the richest sources of natural peptides with promising pharmacological and therapeutic applications. With the reduced costs of RNAseq, scientists now heavily rely on venom gland transcriptomes for the mining of novel bioactive conopeptides, but the bioinformatic analyses often hamper the discovery process.<h4>Results</h4>Here, we present ConoDictor 2.0 as a standalone and user-friendly command-line program. We have updated the program originally published ...[more]

PMID: 36700089

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Dataset Information

Improved prediction of conopeptide superfamilies with ConoDictor 2.0.

Motivation

Results

Availability and implementation

Supplementary information

Publications

Improved prediction of conopeptide superfamilies with ConoDictor 2.0.

Similar Datasets

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