PepTraq: a toolbox for in silico data mining and fast sequence filtering

• Published in: Amino acids Vol. 55; no. 5; pp. 709 - 712
• Main Authors: Zanuttini, Bruno, Henry, Joël, Couronne, Christophe, Ouali, Abdelkader, Robert, Véronique, Zatylny-Gaudin, Céline
• Format: Journal Article
• Language: English
• Published: Vienna Springer Vienna 01-05-2023; Springer Nature B.V; Springer Verlag
• Subjects: Amino acids; Analytical Chemistry; Animal models; Annotations; Applications programs; Biochemical Engineering; Biochemistry; Biologists; Biology; Biomedical and Life Sciences; Brief Report; Computer Science; Data mining; Data processing; Genomes; Life Sciences; Mass spectrometry; Mass spectroscopy; Molecular weight; Multiple criterion; Neurobiology; Peptides; Proteins; Proteomics; Scientific imaging; Software; Source code; Transcriptomes; Sequence filtering; Data processing; Proteomics; Transcriptome; In silico analysis
• ISSN: 0939-4451; 1438-2199
• DOI: 10.1007/s00726-023-03251-y

The development of de novo sequencing tools has led to the massive production of genomes and transcriptomes from many unconventional animal models. To tackle this huge flow of data, PepTraq brings together many functionalities generally scattered in multiple tools, so that sequences can be filtered on the basis of multiple criteria. It is particularly suitable for the identification of non-annotated transcripts, re-annotation, extraction of secretomes, neuropeptidomes, targeted search for peptides and proteins, preparing specific proteomics/peptidomics fasta files for mass spectrometry (MS) applications, MS data processing, etc. PepTraq is developed in Java, and is available as a desktop application that can be downloaded from
https://peptraq.greyc.fr
. It is also available as a web application at the same URL for processing small files (10–20 MB). The source code is open under a CeCILL-B licence.