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ProtoNet Tools

ProtoNet Version 6.1 offers automatic hierarchical classification of proteins. Proteins are processed using a novel clustering algorithm which relies on their sequence distances. The ProtoNet classification hierarchically partitions the protein space into clusters of similar proteins. The lower a cluster is situated in its tree, the smaller it is and the more similar are its proteins to each other. Browsing the clustering hierarchy can provide insight as to function and structure of proteins.

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ProtoNet Tools | protonet.cs.huji.ac.il Reviews

<META> DESCRIPTION

ProtoNet Version 6.1 offers automatic hierarchical classification of proteins. Proteins are processed using a novel clustering algorithm which relies on their sequence distances. The ProtoNet classification hierarchically partitions the protein space into clusters of similar proteins. The lower a cluster is situated in its tree, the smaller it is and the more similar are its proteins to each other. Browsing the clustering hierarchy can provide insight as to function and structure of proteins.

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1 ProtoLevel

2 ProtoDistance

3 proteins

4 clusters

5 ProtoNet

6 cluster

7 protein

8 ProtoMap

9 swissprot

10 uniprotkb/swiss-prot

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ProtoNet Tools | protonet.cs.huji.ac.il Reviews

https://protonet.cs.huji.ac.il

ProtoNet Version 6.1 offers automatic hierarchical classification of proteins. Proteins are processed using a novel clustering algorithm which relies on their sequence distances. The ProtoNet classification hierarchically partitions the protein space into clusters of similar proteins. The lower a cluster is situated in its tree, the smaller it is and the more similar are its proteins to each other. Browsing the clustering hierarchy can provide insight as to function and structure of proteins.

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protonet.cs.huji.ac.il

1

ProtoNet Tools

http://protonet.cs.huji.ac.il/index.php

Returns rich information about a protein. Paste your protein sequence and get the ProtoNet cluster. Protein Sequence Alignment (BLAST). Displays sequence alignment for two proteins. Check protein in cluster. Testing whether a protein belongs to a given cluster. Get ProtoNet clusters by keywords. Get ProtoNet clusters by cluster name. Get cluster card by cluster ID. Vertical perspective, returns information about a ProtoNet cluster. Get the lowest common cluster of two proteins.

2

ProtoNet: Get clusters by "Cluster Name"

http://protonet.cs.huji.ac.il/tool_cluster_name.php?global=1

Protonet Tools get clusters by cluster name. Get clusters by Cluster Name:. Nter exact keyword name. CATH, ENZYME, GO, Gene name, InterPro, Microarrays, PDB, Publication journals, Publication years, SCOP, Taxonomy, UniProt):. Check here to allow for inexact keyword matches, or to search by keyword ID / accession numbers (might take a while to process). Switch to the advanced mode. Hebrew University, Jerusalem, Israel. proto@cs.huji.ac.il.

3

ProtoNet: Get Alignment (provides Blast Sequence Alignment)

http://protonet.cs.huji.ac.il/tool_blast.php?global=1

Pg exec() [ function.pg-exec. No PostgreSQL link opened yet in /a/fr-05/vol/lab/proto/www-prod/global functions/inc global constants.php. Pg exec() [ function.pg-exec. No PostgreSQL link opened yet in /a/fr-05/vol/lab/proto/www-prod/global functions/inc global constants.php. Protonet Tools protein sequence alignment. Protein Sequence Alignment (BLAST):. Isplays sequence alignment for two proteins. ID (eg. AACT HUMAN) or accession number (e.g.P24595). Protein-ID (e.g.X68737). Switch to the advanced mode.

4

ProtoNet Tools

http://protonet.cs.huji.ac.il/index.php?global=1&advanced_search=yes

Returns rich information about a protein. Paste your protein sequence and get the ProtoNet cluster. Protein Sequence Alignment (BLAST). Displays sequence alignment for two proteins. Check protein in cluster. Testing whether a protein belongs to a given cluster. Get ProtoNet clusters by keywords. Get ProtoNet clusters by cluster name. Get cluster card by cluster ID. Vertical perspective, returns information about a ProtoNet cluster. View ProtoNet at specific ProtoLevel.

5

ProtoNet: Get the lowest common cluster of two proteins

http://protonet.cs.huji.ac.il/tool_lowest_cluster.php?global=1

Pg exec() [ function.pg-exec. No PostgreSQL link opened yet in /a/fr-05/vol/lab/proto/www-prod/global functions/inc global constants.php. Pg exec() [ function.pg-exec. No PostgreSQL link opened yet in /a/fr-05/vol/lab/proto/www-prod/global functions/inc global constants.php. Protonet Tools get the lowest common cluster of two proteins. Get the lowest common cluster of two proteins:. ID (eg. AACT HUMAN) or accession number (e.g.P24595). Protein-ID (e.g.X68737). Switch to the advanced mode.

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pandora.cs.huji.ac.il

Pandora

http://pandora.cs.huji.ac.il/index.php

Protein ANnotation Diagram ORiented Analysis. The Sudarsky Center for Computational Biology. The Hebrew University of Jerusalem. Welcome to Pandora version 4.2! In order to study of proteins you can choose from the top menubar:. Study a set of proteins that share an annotation. Study your own set of proteins including quantitative data. Blast a sequence and view the results in PANDORA. Match list of mass spectrometry-derived (MS) peptides to the corresponding proteins and analyze these proteins in PANDORA.

pandora.cs.huji.ac.il

Pandora

http://pandora.cs.huji.ac.il/userset.php

Protein ANnotation Diagram ORiented Analysis. The Sudarsky Center for Computational Biology. The Hebrew University of Jerusalem. Study your own set of proteins ( see help. For further information on file formats etc, see the help sections on input methods. And on user properties. Or you may also load sample data:. Simple list of Protein IDs. Protein IDs with user properties (CSV). Protein IDs with user properties (tab delimited). SwissProt/TrEMBL protein accession numbers. GenBank gene accession numbers.

pandora.cs.huji.ac.il

Pandora

http://pandora.cs.huji.ac.il/keyword.php

Protein ANnotation Diagram ORiented Analysis. The Sudarsky Center for Computational Biology. The Hebrew University of Jerusalem. Study a set of proteins that share a keyword/annotation:. You can study all proteins that share a certain function, structure, biological pathway, cellular localization, etc ( see help. Or part of keyword / auto-completion with 4 characters). Updated Jan. 31st 2010 - Pandora. The Hebrew University of Jerusalem. This site is best viewed with Firefox.

clantox.cs.huji.ac.il

ClanTox

http://clantox.cs.huji.ac.il/about.php

A Classifier of Animal Toxins. The Sudarsky Center for Computational Biology. The Hebrew University of Jerusalem. Toxins are proteins that are present in animal venom. They are extremely diverse in terms of sequence, structure and function. Toxins include several types of proteins such as ion channel inhibitors, phospholipases, disintegrins and others. To understand what these numbers signify, we must first explain the prediction process (see figure). Sequences given to ClanTox are first transformed ...

clantox.cs.huji.ac.il

ClanTox

http://clantox.cs.huji.ac.il/faq.php

A Classifier of Animal Toxins. The Sudarsky Center for Computational Biology. The Hebrew University of Jerusalem. Q: What is the standard deviation good for? Q: I got a positive score for my sequence, how can I tell whether the protein is toxin or toxin-like? Q: A sequence that I entered was classified as toxin or toxin-like. What does this mean? Q: In order to test your classifier, I entered a long sequence of cysteines and got a positive score. Is this bug? Q: What kind of classifiers do you use? A: Ge...

clantox.cs.huji.ac.il

ClanTox

http://clantox.cs.huji.ac.il/tech.php

A Classifier of Animal Toxins. The Sudarsky Center for Computational Biology. The Hebrew University of Jerusalem. P3 - Toxin-like (mean score 0.2 or mean score 2*SD). P2 - Probably toxin-like (mean score 0.2 or 2*SD mean score SD). P1 - Possibly toxin-like (mean score -0.2 and mean score. N - Probably not toxin-like (mean score. Scheme of the meta-classifier underlying ClanTox. Results for the classifier performance. S locus-related glycoprotein 1 binding pollen coat. Whey acidic protein, core region.

proteus.cs.huji.ac.il

ProTeus | Help

http://www.proteus.cs.huji.ac.il/glossary.php

The average length of the proteins who intersect with the assigned annotation. The size of a ProtoNet cluster. Is defined as the number of proteins in this cluster. Connection ratio is defined as the fraction of pairs of proteins from the set of proteins who intersect with the assigned annotation that have a BLAST E-score better than 1.0, out of the total number of pairs. Gapped protein signature groups were allowed to span 3-10 amino acids in length and to include one undetermined amino acid. The ProtoN...

proteus.cs.huji.ac.il

ProTeus | BLAST your protein

http://www.proteus.cs.huji.ac.il/tool_blast_prot.php

This is a specialized BLAST version tuned for short sequences that uses the BLAST algorithm to search for signatures on the termini of the user's protein sequence. This BLAST option allows detection of signatures that are degenerate or include multiple GAPS. Please enter a sequence. Of at least 20 amino acids. SwissProt version 40.28. SwissProt version 41.21 TrEMBL.

proteus.cs.huji.ac.il

ProTeus | PROtein TErminUS. An archive of functional signatures in protein termini

http://www.proteus.cs.huji.ac.il/index.php

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 signatures in termini of proteins. ProTeus, now includes over 1 Million protein sequences. ProTeus offers five search options:. View all collected protein signature groups. Search by an annotation. Returns a list of protein signature groups that matches the entered annotation. Search for a signature. This is a specialized BL...

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ProtoNet Tools

Returns rich information about a protein. Paste your protein sequence and get the ProtoNet cluster. Protein Sequence Alignment (BLAST). Displays sequence alignment for two proteins. Check protein in cluster. Testing whether a protein belongs to a given cluster. Get ProtoNet clusters by keywords. Get ProtoNet clusters by cluster name. Get cluster card by cluster ID. Vertical perspective, returns information about a ProtoNet cluster. Get the lowest common cluster of two proteins.

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