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Showing 20 records out of 359 total
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Categories: similarity search/alignment, similarity search - Software type(s): website - tool
The Basic Local Alignment Search Tool (BLAST) finds regions of local similarity between sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches. BLAST can be used to infer functional and evolutionary relationships between sequences as well as help identify members of gene families.
keywords: sequence alignment
Categories: similarity search/alignment, similarity search - Software type(s): website - tool
BLAST search on protein sequence databases
keywords: sequence alignment
Categories: similarity search/alignment, similarity search - Software type(s): website - tool
Converts BLAST output from NCBI to FASTA format.
keywords: conversion tool
Categories: evolutionary biology - Software type(s): website - tool
A modified BLAST, designed to query ortholog group data. It treats each ortholog group as a unit, and instead of providing a ranked list of individual sequence hits, it organizes and ranks the results by ortholog groups, which is often a much more desirable format for functional inference or evolutionary studies.
Categories: proteomics, (similarity search/alignment), genomics, (sequence alignment) - Software type(s): website, CLI - tool
Boxshade is a program for creating good looking printouts from multiple-aligned protein or DNA sequences.
keywords:
Categories: genomics, (similarity search), evolutionary biology - Software type(s): CLI - tool
BUSCO (Benchmarking Universal Single-Copy Orthologs) provides measures for quantitative assessment of genome assembly, gene set, and transcriptome completeness based on evolutionarily informed expectations of gene content from near-universal single-copy orthologs.
Categories: structure analysis - Software type(s): website - tool
CAMEO continuously evaluates the accuracy and reliability of protein structure prediction methods in a fully automated manner. CAMEO currently assesses predictions in two categories (3D protein structure modeling and ligand binding site residue predictions). The project is open to everyone and has been used by several method developer groups to benchmark and monitor their servers and new developments.
Categories: proteomics, glycomics - Software type(s): website - database
CAZy is a dedicated family classification system correlating structure and molecular mechanism of carbohydrate-active enzymes. It describes the families of structurally-related catalytic and carbohydrate-binding modules (or functional domains) of enzymes that degrade, modify, or create glycosidic bonds.
Categories: genomics, evolutionary biology - Software type(s): website - database/tool
CEGA (Conserved Elements from Genomic Alignments) provides access to precomputed sets of conserved sequences from different species and at different levels of the vertebrate phylogeny.
Categories: systems biology - Software type(s): website, databases files - database
The Cellosaurus is a knowledge resource on cell lines. It attempts to describe all cell lines used in biomedical research, including immortalized cell lines, naturally immortal cell lines (ie stem cell lines), finite life cell lines when those are distributed and widely used, vertebrate cell lines with an emphasis on human, mouse and rat cell lines, and invertebrate (insect and tick) cell lines.
Categories: proteomics, (protein structure) - Software type(s): website - tool
This server predicts secondary structure of protein from the amino acid sequence. In this server, Chou & Fasman algorithm has been implemented.
Categories: genomics, (characterisation/annotation) - Software type(s): website, CLI - tool
The ChIP-Seq tools are used to analyze ChIP-seq data and other types of mass genome annotation data (MGA).The programs are: a feature correlation tool (ChIP-cor); a tag centering tool (ChIP-center); a signal peak detection tool (ChIP-peak and a partitioning tool (ChIP-part)
Categories: proteomics, (protein modifications) - Software type(s): website - tool
The ChloroP server predicts the presence of chloroplast transit peptides (cTP) in protein sequences and the location of potential cTP cleavage sites.
Categories: proteomics, (protein structure), structure analysis, medicinal chemistry - Software type(s): website - tool
Directory of computational drug design tools, containing many links to databases, chemical structure representation, molecular modeling, homology modeling, binding site prediction, docking, screening, target prediction, ligand design, binding free energy estimation etc.
Categories: proteomics, (similarity search/alignment) - Software type(s): website - tool
Align two or more protein sequences on the UniProt web site using ClustalOmega.
keywords: sequence alignment
Categories: proteomics, (similarity search/alignment), genomics, (sequence alignment) - Software type(s): website, CLI, GUI - tool
Multiple alignment of nucleic acid and protein sequences.
Categories: proteomics, (similarity search/alignment), genomics, (sequence alignment) - Software type(s): website - tool
ClustalW is a general purpose multiple sequence alignment program for DNA or proteins
keywords: sequence alignment
Categories: proteomics, (similarity search/alignment), genomics, (sequence alignment) - Software type(s): website - tool
ClustalW2 is a general purpose multiple sequence alignment program for DNA or proteins.
keywords: sequence alignment
Categories: evolutionary biology - Software type(s): website - tool
The Coev-Web platform is a user-friendly interface of the command-line program Coev. The platform allows the evaluation of coevolving positions and their evolutionary profile based on the aligned sequences and a phylogenetic tree. It can also simulate coevolving pairs of positions along a given phylogenetic tree.
Categories: proteomics, (sequence sites, features and motifs) - Software type(s): website - tool
This program delineates coiled-coil domains in otherwise globular proteins, such as the leucine zipper domains in transcriptional regulators, and to predict regions of discontinuity within coiled-coil structures, such as the hinge region in myosin.
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