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Welcome to the GenomeWeb Protein General Sequence Analysis Analysis Search for:

NCSA BIOLOGY WORKBENCH
MOWSE - search by molecular weight fingerprint
NetOglyc - Prediction of Mucin type O-glycosylation sites
Prediction of GlcNAc O-glycosylation site in Dictyostelium discoideum pr
PSORT - Analyze and predict protein sorting signals.
PROPSEARCH - database query by amino acid composition
CombSearch - interface to query several protein identification tools
Peptide MW Calculator
Compute pI/Mw tool
Physico-chemical profiles
ProtParam tool
PEST - identify proteins with short half-lives
SAPS - Statistical Analysis of Protein Sequences
CBRG at ETHZ
PeptideSearch Database searching by mass spectrometric data
GeneFIND Family Identification System
GeneQuiz
PEDANT - Protein Extraction, Description, and ANalysis Tool
A280/A260 calculator
Pratt Pattern Discovery

Detailed information on the above options

NCSA BIOLOGY WORKBENCH
The Biology Workbench is a point and click WWW interface for an integrated set of programs and database searching tools that allow you to carry out sequence analysis without having to log into a remote computer site.

The service is free to non-commercial researchers (you just need to register). There is a comprehensive demonstration to help you get started.

MOWSE - search by molecular weight fingerprint
You can use this page to submit a MOWSE database search. MOWSE will search the OWL protein database with the protein fragment information, and return the protein(s) which most likely correspond to your peptide-data.

NetOglyc - Prediction of Mucin type O-glycosylation sites
The specificities of the UDP-GalNAc:polypeptide N-acetylgalactosaminyltransferase family which links the carbohydrate GalNAc to the side chain of certain serine and threonine residues in mucin type glycoproteins are presently unknown. The specificity seems to be modulated by sequence context, secondary structure and surface accessibility. The sequence context of glycosylated threonines was found to differ from that of serine, and the sites were found to cluster. Non-clustered sites had a sequence context different from that of clustered sites. Charged residues were disfavoured at position -1 and +3. A jury of artificial neural networks was trained to recognize the sequence context and surface accessibility of 299 known and verified mucin type O-glycosylation sites extracted from O-GLYCBASE. The cross-validated NetOglyc network system correctly found 83 % of the glycosylated and 90 % of the non-glycosylated serine and threonine residues in independent test sets, thus proving more accurate than matrix statistics and vector projection methods.

Prediction of GlcNAc O-glycosylation site in Dictyostelium discoideum pr
The server is at an experimental stage for now, due to the limited dataset of 39 experimentally known sites of glycosylations. They hope to increase the accuracy of the server with availability of more experimental data.

PSORT - Analyze and predict protein sorting signals.
Analyze and predict protein sorting signals coded in amino acid sequences.

PROPSEARCH - database query by amino acid composition
PROPSEARCH reads your amino acid compositional analysis data and performs a protein database query to identify the protein. The result is emailed back to you. Searches take about 20 minutes.

CombSearch - interface to query several protein identification tools
CombSearch provides a unified interface for simultaneous queries to several protein identification programs accessible on the web.

Peptide MW Calculator
This calculates the molecular weight of your peptide.

Compute pI/Mw tool
Compute pI/Mw is a tool which allows the computation of the theoretical pI (isoe lectric point) and Mw (molecular weight) for a protein sequence.

Physico-chemical profiles
This displays the following physico-chemical properties of your sequence.

• antigenicity (Hopp & Woods)
• hydrophobicity
• chain flexibility
• antigenicity (Parker et al.)
• TM regions

ProtParam tool
ProtParam is a tool which allows the computation of various physical and chemica l parameters for a protein sequence.

The computed parameters include the molecular weight, theoretical pI, amino acid composition,

• extinction coefficient,

PEST - identify proteins with short half-lives
Proteins with intracellular half-lives of less than two hours are found to contain regions rich in proline, glutamic acid, serine and threonine (P, E, S and T). These so called PEST regions are generally flanked by clusters of positively charged amino acids.

The PEST search utility identifies possible PEST regions in a submitted probe using the Molecular fraction of the P, E, S and T components, and the hydrophobicity index of the region.

SAPS - Statistical Analysis of Protein Sequences
This program, written by the group of Samuel Karlin, analyses proteins for statistically significant features like charge-clusters, repeats, hydrophobic regions, compositional domains etc. One of its options is to generate self-explanatory output.

CBRG at ETHZ

• AllAll: Related peptide sequences (Trees, ancestral seq., MSA, predictions etc

• AllAllDB: Querying the all-against-all database of SwissProt
• MassSearch: Searching SwissProt or EMBL by protein mass after digestion
• NuclPepSearch: Searching SwissProt for a nucleotide sequence
• PepPepSearch: Searching SwissProt for a peptide sequence
• TreeGen: Tree generation from distance data
• darwin: Run a Darwin program
• PredictGenes: predict and verify gene structure by alignment with homologous p

• MultAlign: Multiple sequence alignment tools (recalculate, adjust, optimize, t

• MassDynSearch: Seraches Swissprot with the masses of protein fragments after N
• or C-terminal digestion
• Darwin, a Computational Biochemistry Research Tool

PeptideSearch Database searching by mass spectrometric data
This is an advanced tool for protein database searching by mass spectrometric data, such as peptide mass maps or (partial) amino acid sequences.

GeneFIND Family Identification System
The GeneFIND family identification system aims at high-throughput full-scale gene family identification, by taking advantages of the strengths of various sea rch methods and incorporating ProClass family information. Multi-level filters are u sed, starting the fastest MOTIFIND neural networks, followed by BLAST search, SSEARCH dynamic programming, and motif pattern search. The current implementation allows large-scale identification of 942 protein families.

GeneQuiz
Genequiz provides highly automated analysis of biological sequences.

GeneQuiz derives functional annotation for protein sequences and provides supporting evidence, including family alignments.

PEDANT - Protein Extraction, Description, and ANalysis Tool
PEDANT is a software system for completely automatic and exhaustive analysis of protein sequence sets - from individual sequences to complete genomes.

• Exhaustive functional and structural classification of

• Functional assignment of ORFs on the basis of FASTA2 similarity searches supplemented by detection of PROSITE patterns and motifs and comparisons with conserved sequence blocks

• Automatic attribution of sequences with significantly related PIR entries to one of the PIR super-families

• Functional classification of gene products through similarity searches against several curated master gene sets from bacteria and yeast with manually assigned functional classes

• Extraction of available 3D information through Smith-Waterman similarity comparisons of every sequence with the STRIDE database of secondary structure assignments

• Secondary structure and transmembrane region predictions

• Detection of low-complexity and coiled coil regions

A280/A260 calculator
This can be used to calculate the molecular weight (using average isotopic mass), extinction coefficient, the concentration, and the formal charge of a protein.

Pratt Pattern Discovery
Pratt is a tool that allows the user to search for patterns conserved in a set of protein sequences. The user can specify what kind of patterns should be searched for, and how many sequences should match a pattern to be reported.