Appendix for UniNovo : a universal tool for de novo peptide sequencing
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UniNovo: a universal tool for de novo peptide sequencing
MOTIVATION Mass spectrometry (MS) instruments and experimental protocols are rapidly advancing, but de novo peptide sequencing algorithms to analyze tandem mass (MS/MS) spectra are lagging behind. Although existing de novo sequencing tools perform well on certain types of spectra [e.g. Collision Induced Dissociation (CID) spectra of tryptic peptides], their performance often deteriorates on oth...
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We have developed and implemented a framework for de novo sequencing of peptides using tandem mass spectrometry data. It first cleans the input spectrum with a number of data cleaning algorithms (“grass mowers”), followed by a sequencing algorithm that is a modification of a dynamic programming algorithm introduced in [CKT00]. In first experiments, our prototype performs well (but not better) i...
متن کاملClustering 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...
متن کاملOpen - 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...
متن کاملMass 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...
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