Search Results for "proteins"
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Showing 13 open source projects for "proteins"
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TaxOnTree
A program for associating taxonomic information in a phylogenetic tree
TaxOnTree is a phylogenetic program for associating Taxonomic information in a phylogenetic tree. The output is a NEX format tree file configured to be opened in FigTree, that users can promptly color by any taxa or by the ancestrality shared by sequences with query. Input can be a Fasta formatted file to be used in a BLAST search or a list of sequences represented by their identifiers (UniProtAC or NCBI gi), if a cluster is already available. Also, a newick file produced with user software... -
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selectseq
Get specific sequences from a FASTA or FASTQ file.
A command-line utility to manipulate biological sequences from a FASTA or FASTQ file. It can, given a list of identifiers, get only a subset of the sequences (or their complement, i.e., sequences NOT in the list). Can also get sequence number N only. Compressed sequences files are supported if readable by zcat. -
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PanOCT
Pan-genome Ortholog Clustering Tool
PanOCT, Pan-genome Ortholog Clustering Tool, is a program written in PERL for pan-genomic analysis of closely related prokaryotic species or strains. Unlike traditional graph-based ortholog detection programs, it uses micro synteny or conserved gene neighborhood (CGN) in addition to homology to accurately place proteins into orthologous clusters. -
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datasw
datasw, a tool for rapid processing of HPLC-SAXS data.
... experiment using a sliding window of a user-specified size, calculates overall parameters (I(0), Rg, Dmax and MW) and predicts the folding state (folded/unfolded) of the sample. Applications of DATASW are illustrated for several proteins with various oligomerization behaviors recorded at different beamlines. If you use DATASW in your work, please, cite: Shkumatov A.V. & Strelkov S.V. (2015) Acta Cryst. D71, 1347–1350 -
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Hamstr
A tool for directed ortholog search in ESTs and proteins
HaMStR has moved to https://github.com/bionf/hamstr where it is now part of the HaMStR-OneSeq package. HaMStR is a profile hidden Markov model based tool for a directed ortholog search in EST or protein sequence data. The program takes a pre-defined core group of orthologous sequences (core orthologs) and a set of sequences from a search taxon as input. HaMStR then combines in a two-step strategy a pHMM based search and a reverse search via BLAST to extend the core ortholog group with... -
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NGS-TOOLBOX
Handy tools to process/analyze next generation sequencing (NGS) data
... purposes you can cite the following methods paper: Rosenkranz D, Han CT, Roovers EF, Zischler H, Ketting RF. Piwi proteins and piRNAs in mammalian oocytes and early embryos: From sample to sequence. Genomics Data 2015 5:309-313. -
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The Protein Similarity Network
Human protein similarity network used to predict drug safety.
This is the protein similarity network - PSIN. Here, the nodes are human proteins and they are linked only if they share considerable sequence similarity. We found that this network is particularly useful to distinguish approved from problematic drug-targets. Here you also find the complete set of programs and datasets we used for this purpose. Free to help further test and develop this project. Your help and expertise are much appreciated ! If you have any questions, please do... -
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CViT - Chromosome Viewing Tool. A collection of Perl scripts that enable quick visualizations of features on linkage groups, psuedochromosomes or cytogenetic maps. Intended for whole-genome views of data but can be used to create images of single chromosomes/linkage groups, contigs, or BACs, or even proteins -- any feature that has a location on a backbone. Handles most standard genetic/genomic coordinate systems. Reads GFF3 data and produces a PNG or SVG image.
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Just_Annotate_My_Genome
Comprehensively annotate your non-model species genome.
Uses an existing exonerate output or just predicted proteins (e.g. from Transdecoder or just a FASTA file) to prepare gene prediction inputs for Augustus, SNAP and geneid. Exonerate is run (enabled via AAT) if it is not provided. GTF file is produced to judge quality of annotation. Sorts out high quality alignments from those that don't meet the criteria. -
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FIAP
Fully Integrated Annotation Pipeline
FIAP (Fully Integrated Annotation Pipeline) is a fast bacterial genome multithreading annotation pipeline written in Perl that detects genes coding for proteins, tRNAs, and rRNAs (5S, 16S and 23S). FIAP also allows users to include an infinite number of custom databases. This feature is extremely valuable because it allows users to add a personal “flavor” to the annotation and optimize the process for a specific bacterial genome. FIAP can annotate single and multiple sequences, which allows... -
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A rule-based modelling framework for allosteric proteins and biochemical networks.
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TransposonPSI is an analysis tool to identify protein or nucleic acid sequence homology to proteins encoded by diverse families of transposable elements.
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Finds conserved regions in the aminoacid sequences of proteins by looking at multiple sequences of a protein family. Also allows comparison between user-defined groups of protein sequences.
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