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Pfam
Alignments and hidden Markov models covering many protein domains. Pfam is a large collection of multiple sequence alignments and hidden Markov models covering many common protein families. Pfam version 10.0 (July 2003) contains alignments and models for 6190 protein families, based on the Swissprot 41.10 and SP-TrEMBL 23.15 protein sequence databases.


PlantsP
Functional genomics of plant phosphorylation.

DPL Forum: Too few categories!


TIGRFAMs and Genome Properties tools for the assignment of molecular function and biological process in prokaryotic genomes. TIGRFAMs is a collection of protein family definitions built to aid in high-throughput annotation of specific protein functions. TIGRFAMs are protein families based on Hidden Markov Models or HMMs, which can classify numerous proteins according to their specific molecular functions. The Genome Properties system is particularly useful as a generator of phylogenetic profiles, through which new protein family functions may be discovered. <pubmed argument="TIGRFAM">17151080</pubmed>



3matrix - motifs in three dimensions
Lin Lu. , Steven P. Bennett. and Douglas L. Brutlag. Department of Biochemistry. , Stanford University. Important Note: 3matrix requires the Chime plugin. Instruction for search by sequence.. Expectation value threshold for search by ...
Web-based sequence motif visualization system that displays sequence motif information in its appropriate three-dimensional (3D) context. Users can enter sequences, keywords, structures or sequence motifs to generate visualizations.


CysView - Automated Protein Classification by Disulfide Connectivity
CysView - Automated Protein Classification by Disulfide Connectivity Patterns. Upload a text file *.txt files only (. OR enter data Predict connectivity pattern for entries without disulfide bridge information. (Note: This can take some ...


GeneFIND Server at NBRF-PIR
GeneFIND Web Server The GeneFIND World Wide Web Server provides on-line family identification of query sequences and keyword search for information retrieval of protein families. The search is based on a collection of databases and search ...


ProTarget - Target Selection
Introduction. Query. References. About. Introduction ProTarget offers a novel method for the prediction of new structural superfamilies. Given a new sequence, it is inserted into a hierarchical clustering of the protein space, and its ...


FingerPRINTScan
Site search ?. .. .. PROTEIN FUNCTIONAL ANALYSIS. Help Index. General Help. Formats. Gaps. Matrix. References. FingerPRINTScan Help. FingerPRINTScan Submission Form Search against FingerPRINTScan with a protein query sequence to identify ...


PP1
Introduction *. This web site is a new tool to identify putative Protein Phosphatase 1 (PP1) binding proteins. This subgroup-site of the Swissprot library contains protein sequences selected on the basis of the simultaneous presence of two ...


Family Pairwise Search
Family Pairwise Search (FPS) is a method for scoring a query sequence against a family of sequences. (Note: the query "sequence" may alternatively be a sequence, a GCG profile or a BLAST checkpoint file.) FPS compares the query sequence ...


ProTeus | PROtein TErminUS. An archive of functional signatures in
P R O t e i n T E r m i n U S About. Help. Feedback. ProTeus (PROtein TErminUS) is a tool for identification of short linear signatures in protein termini. It is based on a positional-based search method for revealing short significant ...


Picasso: protein families
Get for ?. unified family: cluster: sequence: identifier:. unified family: view members of a unified family (e.g., 1234). cluster: view multiple alignments of a cluster (e.g., CLUS_1234_1). sequence: sequence report with domains/motifs ...


Submit a Sequence
PeCoP. PSI-BLAST your sequence to find Persistently Conserved Positions Please wait until you have received the results of one job before you submit another. Thank you. Bioinformatics.Org track.


PSCAN
PSCAN. : Scans proteins using PRINTS (EMBOSS). your e-mail ( = conditionally required) Input section. Required section. Output section. Input section Minimum number of elements per fingerprint (-emin) outfile (-outfile) [Return to the main ...


P-val FingerPRINTScan
Mail any comments, bugs, or suggestions to: scordis@bioinf.man.ac.uk.


WebProAnalyst
WebProAnalyst Quantitative Structure-Activity Relationship analysis of related protein families Enter sequence alignment in FASTA format (from screen or from file): Protein activity values (for example, 1.5 -10 ? 45.66 etc): Analysis: ...


Top
TMMOD Transmembrane protein topology prediction server. Kahsay, R., Liao, L., Gao, G. (Nov 2004). An Improved Hidden Markov Model for Transmembrane Protein Topology Prediction. ICTAI'04 (16th IEEE International Conference on Tools with ...


Brutlag Bioiunformatics Group - Licensed Software Download - 3matrix - Protein Structure Visualization System for Conserved Sequence Motifs
Software Distribution:.3matrix 1.0 (March, 2003).. Data Files:.pdb-03-2003_1.tar (Large File: ~504 MB). .pdb-03-2003_2.tar (Large File: ~1069 MB). .pdb-03-2003_3.tar (Large File: ~770 MB). .pdb-03-2003_4.tar (Large File: ~275 MB).. To ...


DiffTool Main Page
DiffTool Main Page. Help. Select proteins:. Cluster database built with: Search: a (part of a) keyword in protein annotation a protein name Enter an annotation keyword or a protein name: (e.g. keyword 'rna methylase' or protein name ...


Protein Link Explorer [ PLEX ]
Welcome to the Protein Link Explorer (PLEX). Given an amino acid sequence or its GenBank sequence identifier, PLEX allows a phylogenetic profile to be constructed, which can subsequently be compared to profiles of upto 350,111 other ...


Search Prints With a Nucleotide Sequence
ACCESSION P-VALUE MASK REPEAT REGIONS PASTE YOUR SEQUENCE HERE(numbers and whitespace are ignored)For help, click here. Alternatively, upload a file of nucleotide sequences (FASTA format) for batch analysis.N.B. Entry of a file in this ...


MOTIF: Searching Protein and Nucleic Acid Sequence Motifs
MOTIF Search Please change your bookmark! In August 2004 the GenomeNet addresses were changed from ".genome.ad.jp" to ".genome.jp". The old form is no longer automatically redirected. MOTIF: Searching Protein and Nucleic Acid Sequence ...


GIST: Support Vector Machine 1.0 - Data submission
The svm software was developed by William Stafford Noble. in the Department of Genome Sciences and Computer Science at the University of Washington and Paul Pavlidis. in the Genome Center at Columbia University. The web server was built ...


SVMMER
SVMMER. SVMMER

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