I. Protein identification and characterization
II. Translation of DNA to protein sequence
III. Similarity search and sequence alignment.
IV. Motif and domain scan
V. Protein interaction and network
VI. Post-translational modifications (PTMs) search
VII. Topology prediction
VIII. Primary, secondary, and tertiary structure analysis
Mascot:
Peptide mass fingerprinting. - by Matrix Science Ltd., London
ProFound:
Peptide mass fingerprinting. - by The Rockefeller University
ProteinProspector:
MS-Fit, MS-Tag, MS-Digest, MS-Seq, etc. - by UCSF
PeptideCutter:
predicts potential cleavage sites cleaved by proteases or chemicals in a given protein sequence. - by ExPASy
PeptIdent:
a tool that allows the identification of proteins using pI, Mw and peptide mass fingerprinting data. - by ExPASy
TagIdent:
a tool that allows the identification of proteins by matching a short sequence tag of up to 6 amino acids against proteins in the SWISS-PROT/TrEMBL databases close to a given pI and Mw. - by ExPASy
Compute pI/Mw:
a tool which allows the computation of the theoretical pI (isoelectric point) and Mw (molecular weight) for a list of SWISS-PROT and/or TrEMBL entries or for a user entered sequence. - by ExPASy
MW, pI, Titration Curve:
a tool which allows the computation of the theoretical pI and Mw, and a titration curve is provided. - by L'Atelier BioInformatique de Marseille
Translate:
EMBOSS Transeq:
translates nucleic acid sequences to the corresponding peptide sequence. It can translate in any of the 3 forward or three reverse sense frames, or in all three forward or reverse frames, or in all six frames. - by EMBL-EBI
Backtranslation:
a tool that allows the backtranslation of proteins with custom codon usage tables fine-tuned down to the single nucleotide. - by Entelechon
NCBI BLAST:
BLink:
A systematic and automatic link to the BLAST search result. - by NCBI
SIB BLAST:
This NCBI BLAST2 service is maintained by the Swiss Institute of Bioinformatics
SIM - Alignment:
a program which finds a user-defined number of best non-intersecting alignments between two protein sequences or within a sequence. - by ExPASy
DIALIGN:
a program for multiple alignment. - by The BiBiServ Sequence Analysis Department, University of Bielefeld, Belgium
MUSCA:
an algorithm for constrained alignment of multiple data sequences. - by IBM
Scansite:
ScanProsite:
a program allows to scan a protein sequence (either from SWISS-PROT or TrEMBL or provided by the user) for the occurrence of patterns and profiles stored in the PROSITE database, or to search protein databases with a user-entered pattern. - by ExPASy
Motif Scan:
Motif scanning means finding all known motifs that occur in a sequence. - by SIB
Pfam:
Protein families database of alignments and HMMs. - by Sanger Institute, UK
SMART:
SMART (a Simple Modular Architecture Research Tool) allows the identification and annotation of genetically mobile domains and the analysis of domain architectures. - by EMBL
InterProScan:
FindMod:
GlycoMod:
a tool that can predict the possible oligosaccharide structures that occur on proteins from their experimentally determined masses. The program can be used for free or derivatized oligosaccharides and for glycopeptides. - by ExPASy
NetPhos:
The NetPhos WWW server produces neural network predictions for serine, threonine and tyrosine phosphorylation sites in eukaryotic proteins. - by CBS
Kyte-Doolittle Hydropathy Plots:
TMpred:
The TMpred program makes a prediction of membrane-spanning regions and their orientation. The algorithm is based on the statistical analysis of TMbase, a database of naturally occuring transmembrane proteins. The prediction is made using a combination of several weight-matrices for scoring. - by EMBnet.org
Membrane Protein Explorer:
A tool for exploring the topology and other features of membrane proteins by means of hydropathy plots, using thermodynamic principles. - by Stephen White Laboratory at UC Irvine
SubLoc:
A tool for the prediction of protein subcellular localization. - by Tsinghua University
TargetP:
Prediction of subcellular location. - by CBS
TMAP:
Transmembrane prediction based on multiple sequence alignment. - by Karolinska Institutet
ProtScale
An amino acid scale is defined by a numerical value assigned to each type of amino acid. The most frequently used scales are the hydrophobicity or hydrophilicity scales and the secondary structure conformational parameters scales, but many other scales exist which are based on different chemical and physical properties of the amino acids. - by ExPASy
ProtParam:
COILS:
a program that compares a sequence to a database of known parallel two-stranded coiled-coils and derives a similarity score. - by EMBnet.org
AGADIR:
An algorithm to predict the helical content of peptides. - by EMBL
Jpred:
A consensus method for protein secondary structure prediction. - by University of Dundee
PredictProtein:
PredictProtein is a service for sequence analysis, and structure prediction. - by Columbia University
GENO3D:
Automatic modelling of protein 3D structure. - by PBIL Lyon-Gerland
3D-PSSM :
A fast, web-based method for protein fold recognition using 1D and 3D sequence profiles coupled with secondary structure and solvation potential information. - by Imperial College of Science, Technology, and Medicine
Note: These bioinformatic tools are freely-accessed on-line. The list has been made from the tools that are used and prefered in our laboratory. There are several other tools and commercially available softwares that can be applied to a particular bioinformatics-based analysis but are not included into our list. Please feel free to inform us about your search tools and softwares, directly e-mail to webmaster:
thongboonkerd@dr.com
