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.
BLAT on DNA is designed to quickly find sequences of 95% and greater similarity of length 25 bases or more. It may miss more divergent or shorter sequence alignments. It will find perfect sequence matches of 20 bases. BLAT on proteins finds sequences of 80% and greater similarity of length 20 amino acids or more. In practice DNA BLAT works well on primates, and protein blat on land vertebrates.
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)
Clustal Omega is a multiple sequence alignment program for proteins. It produces biologically meaningful multiple sequence alignments of divergent sequences. Evolutionary relationships can be seen via viewing Cladograms or Phylograms.
PipMaker computes alignments of similar regions in two DNA sequences. The resulting alignments are summarized with a "percent identity plot'', or "pip'' for short. MultiPipMaker allows the user to see relationships among more than two sequences. All pairwise alignments with the first sequence are computed and then returned as interleaved pips. Moreover, MultiPipMaker can be requested to compute a true multiple alignment of the input sequences and return a nucleotide-level view of the results.
Multiple Em for Motif Elicitation (MEME) performs motif discovery on DNA, RNA or protein datasets and discovers novel, ungapped motifs (recurring, fixed-length patterns) in your sequences (sample output from sequences). MEME splits variable-length patterns into two or more separate motifs.
Addgene's plasmid repository contains a variety of fluorescent protein plasmids. Use this guide to learn more about the many applications of fluorescent proteins (FPs) and to find the plasmids that are available from Addgene's depositing scientists.
The Global Proteome Machine Database was constructed to utilize the information obtained by GPM servers to aid in the difficult process of validating peptide MS/MS spectra as well as protein coverage patterns. This database has been integrated into GPM server pages, allowing users to quickly compare their experimental results with the best results that have been previously observed by other scientists.
ms-utils.org is a list of free (gratis) software for analysis of mass spectrometry data. It is both a repository and a collection of up-to-date links to different types of freely available software and code snippets for the visualization and analysis of mass spectrometry data with emphasis on automated methods for proteomics and protein analysis.
These programs were developed in the UCSF Mass Spectrometry Facility, which is directed by Dr. Alma Burlingame, Professor of Chemistry and Pharmaceutical Chemistry at UCSF and funded by the NIH National Institute for General Medical Sciences.
X! Hunter is a search engine that compares experimentally observed spectra directly with consensus mass spectra obtained from the GPMDB. It can identify proteins for human, budding yeast, mouse and thale cress samples. Because the sequence modifications and cleavage sites for the peptides in the sequence library are already known, it is not necessary to specify as many parameters for this type of search as in more conventional search engines.
A GPM (Global Proteome Machine) web-based X! Tandem search engine for protein/peptide identification, using mass spectrum files as input. The allowed formats for spectrum files include GAML, mzXML, mzData, DTA, PKL and MGF . The search procedure is controlled by a number of parameters, normally given in an XML file.