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Protein sequence reconstruction software tools | Shotgun metagenomic sequencing data analysis

The determination of protein sequences from a metagenomic dataset enables the study of metabolism and functional roles of the organisms that are present in the sampled microbial community.Source text:(Yang et al., 2015) SFA-SPA: a suffix array based…
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GRASP
Desktop

GRASP Guided Reference-based Assembly of Short Peptides

Identifies the homologs of a given reference protein sequence in a database of…

Identifies the homologs of a given reference protein sequence in a database of short peptide metagenomic sequences. GRASPx is a fast and accurate homology-search program implementing a simultaneous…

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PhyloBot
Web
Desktop

PhyloBot

Makes ancestral sequence reconstruction easy. PhyloBot provides interactive…

Makes ancestral sequence reconstruction easy. PhyloBot provides interactive tools to explore evolutionary trajectories between ancestors, enabling the rapid generation of hypotheses that can be…

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OPAR
Web

OPAR Optimistic Protein Assembly from Reads

Salvages reads from metagenomics datasets which could be distantly related to…

Salvages reads from metagenomics datasets which could be distantly related to another characterized species. OPAR is an online resource that contributes to the discovery and characterization of new…

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ProtASR
Desktop

ProtASR

Infers ancestral protein sequences accounting for selection on protein…

Infers ancestral protein sequences accounting for selection on protein stability. ProtASR generates site-specific substitution matrices through the structurally constrained mean-field substitution…

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SFA-SPA
Desktop

SFA-SPA

Significant computational improvements to the short peptide assembly algorithm…

Significant computational improvements to the short peptide assembly algorithm that make it practical to reconstruct proteins from large metagenomic datasets containing several hundred million reads,…

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SPA
Desktop

SPA Short peptide Assembler

Assembles protein sequences from their constituent peptide fragments identified…

Assembles protein sequences from their constituent peptide fragments identified on short reads. The SPA algorithm is based on informed traversals of a de Bruijn graph, defined on an amino acid…

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