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Showing 20 records out of 363 total
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Categories: genomics, (characterisation/annotation), transcriptomics - Software type(s): website - database/tool
A website to browse miRNA target predictions from the ElMMo algorithm
keywords: miRNA target
Categories: proteomics - Software type(s): website - database/tool
Set of bioinformatics tools, databases and courses
Categories: proteomics, genomics - Software type(s): website - tool
Sequence Translation (Transeq, Sixpack) is used to translate nucleic acid sequence to corresponding peptide sequences. Back-translation (Backtranseq, Backtranambig) is used to predict the possible nucleic acid sequence that a specified peptide sequence has originated from.
keywords: codon, translation
Categories: proteomics, (function analysis) - Software type(s): website - database
ENZYME is a repository of information relative to the nomenclature of enzymes. It is primarily based on the recommendations of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (IUBMB) and it describes each type of characterized enzyme for which an EC (Enzyme Commission) number has been provided.
Categories: genomics, (characterisation/annotation) - Software type(s): website - database/tool
The Eukaryotic Promoter Database is an annotated non-redundant collection of eukaryotic POL II promoters, for which the transcription start site has been determined experimentally. Access to promoter sequences is provided by pointers to positions in nucleotide sequence entries. The annotation part of an entry includes description of the initiation site mapping data, cross-references to other databases, and bibliographic references.
Categories: proteomics, (sequence sites, features and motifs) - Software type(s): website - tool
epestfind allows rapid and objective identification of PEST motifs in protein target sequences. Those proteins share high local concentrations of amino acids proline (P), glutamic acid (E), serine (S), threonine (T) and to a lesser extent aspartic acid (D). It seems that PEST motifs reduce the half-lives of proteins dramatically and hence, that they target proteins for proteolytic degradation
Categories: glycomics - Software type(s): website - tool
Glycan structures submitted to EpitopeXtractor are compared to the complete collection of glycan determinants stored in the Glydin' network (http://glycoproteome.expasy.org/epitopes/). The tool extracts all matching substructures and displays them as SNFG cartoons (Symbol Nomenclature for Glycans (SNFG) described here https://www.ncbi.nlm.nih.gov/glycans/snfg.html) with the option of mapping the results on the Glydin' network.
Categories: genomics, (characterisation/annotation), transcriptomics - Software type(s): website - tool
ESTScan can detect coding regions (CDS) in DNA sequences, even if they are of low quality. It also detects/corrects sequencing errors that lead to frameshifts. ESTScan is not a gene prediction program , nor is it an open reading frame detector. In fact, its strength lies in the fact that it does not require an open reading frame to detect a coding region. The program may miss a few translated amino acids at termini, but detects coding regions with high selectivity and sensitivity.
Categories: evolutionary biology - Software type(s): website - tool
This program maps evolutionary traces to structures
Categories: transcriptomics - Software type(s): GUI - tool
ExpressionView is an R package that provides an interactive environment to explore biclusters identified in gene expression data. A sophisticated ordering algorithm is used to present the biclusters in a visually appealing layout. From this overview, the user can select individual biclusters and access all the biologically relevant data associated with it. The package is aimed to facilitate the collaboration between bioinformaticians and life scientists who are not familiar with the R language.
Categories: proteomics, (protein structure) - Software type(s): website - tool
EzMol is a wizard for protein display and image production, allowing to upload a coordinate file, specify chain style, color background and structures, color or hide cartoons or stick side chains, color surface patches and label residues, as well as render and download the produced image.
Categories: proteomics, (similarity search/alignment), genomics, (similarity search) - Software type(s): website - tool
This tool provides sequence similarity searching against protein databases using the FASTA suite of programs. FASTA provides a heuristic search with a protein query. FASTX and FASTY translate a DNA query. Optimal searches are available with SSEARCH (local), GGSEARCH (global) and GLSEARCH (global query, local database).
keywords: sequence alignment
Categories: genomics - Software type(s): CLI - tool
FastEpistasis is a high performance tool designed to test for epistasis effects when analysing continuous phenotypes. It computes tests of epistasis for a large number of SNP pairs, and is an efficient parallel extension to the PLINK epistasis module.
Categories: genomics, evolutionary biology, population genetics - Software type(s): website, CLI - tool
fast sequential markov coalescent simulation of genomic data under complex evolutionary models
keywords:
Categories: genomics - Software type(s): CLI - tool
Tagger and fetchGWI are tools which allow searching short sequence tags against entire genomes or mRNA reference sequence databases.
Categories: proteomics, (proteomics experiment, function analysis, protein modifications) - Software type(s): website - tool
Predict potential protein post-translational modifications (PTM) and find potential single amino acid substitutions in peptides. The experimentally measured peptide masses are compared with the theoretical peptides calculated from a specified Swiss-Prot/TrEMBL entry or from a user-entered sequence, and mass differences are used to better characterise the protein of interest.
Categories: proteomics, (protein sequences and identification, proteomics experiment, function analysis) - Software type(s): website - tool
Identify peptides that result from unspecific cleavage of proteins from their experimental masses, taking into account artefactual chemical modifications, post-translational modifications (PTM) and protease autolytic cleavage.
Categories: proteomics, (sequence sites, features and motifs) - Software type(s): website - tool
The program scans a protein sequence against the PRINTS Protein Fingerprint Database.
Categories: proteomics, (protein structure) - Software type(s): website - tool
FUGUE is a program for recognizing distant homologues by sequence-structure comparison. It utilizes environment-specific substitution tables and structure-dependent gap penalties, where scores for amino acid matching and insertions/deletions are evaluated depending on the local environment of each amino acid residue in a known structure
Categories: proteomics, (sequence sites, features and motifs, similarity search/alignment), genomics, (sequence alignment) - Software type(s): website - tool
Positional dependent information contents of aligned RNA/DNA or amino acid sequences are useful for the display of consensus sequences and for finding optimal search windows used in sequence analysis. The program calculates the positional information content of mono or poly nucleotides/amino acids from a FASTA file of aligned sequences and writes a Postscript (or encapsulated Postscript, EPS) file that can be viewed and included in text processors
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