AuDeNS: A Tool for Automatic De Novo Peptide Sequencing

AUDENS: a tool for automated peptide de novo sequencing.

We present AUDENS, a new platform-independent open source tool for automated de novo sequencing of peptides from MS/MS data. We implemented a dynamic programming algorithm and combined it with a flexible preprocessing module which is designed to distinguish between signal and other peaks. By applying a user-defined set of heuristics, AUDENS screens through the spectrum and assigns high relevanc...

Appendix for UniNovo : a universal tool for de novo peptide sequencing

Open - pNovo : De Novo Peptide Sequencing with Thousands of 2 Protein

9 ABSTRACT: De novo peptide sequencing has improved remarkably, 10 but sequencing full-length peptides with unexpected modifications is 11 still a challenging problem. Here we present an open de novo 12 sequencing tool, Open-pNovo, for de novo sequencing of peptides 13 with arbitrary types of modifications. Although the search space 14 increases by ∼300 times, Open-pNovo is close to or even ∼10...

Mass Analysis Peptide Sequence Prediction (MAPSP)

UNLABELLED The software tool MAPSP allows the combinatorial prediction of novel short peptides such as hormones with common sequence features. In addition, it assists in de novo sequencing in general. The tool was designed for use in conjunction with the analytical identification method of mass spectrometry (MS) and it can considerably speed-up the analysis of unknowns. AVAILABILITY The web i...

Clustering of Short Read Sequences for de novo Transcriptome Assembly

Given the importance of transcriptome analysis in various biological studies and considering thevast amount of whole transcriptome sequencing data, it seems necessary to develop analgorithm to assemble transcriptome data. In this study we propose an algorithm fortranscriptome assembly in the absence of a reference genome. First, the contiguous sequencesare generated using de Bruijn graph with d...