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Links tagged with 'protein isoforms'

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ASPicTool Content

http://t.caspur.it/ASPIC/

Expression > Splicing
Expression > cDNA, EST, SAGE
Sequence Comparison > Other Alignment Tools

Alternative Splicing Prediction (ASPic) can predict alternative splicing of user submitted genes based on comparative analysis of available transcript and genome data from a variety of species. Results include graphical and tabular views of the splicing patterns of full-length mRNA isoforms compatible with the detected splice sites of the genes as well as structural and functional annotations.

NAR Web Server Issue 2006
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tagsalgorithms alternative splicing animals base sequence benchmarking exons gene expression profiling genomics heterogeneous-nuclear ribonucleoproteins humans introns messenger rna molecular computers molecular models protein isoforms rna splice sites sequence alignment software design software validation

ASPicDBDatabase Content

http://www.caspur.it/ASPicDB/

Human Genome > Databases
Protein > Databases

ASPicDB provides a unique annotation resource of human protein variants generated by alternative splicing. A total of 256,939 protein variants from 17,191 multi-exon genes have been extensively annotated through machine learning tools providing information of the protein type (globular and transmembrane), localization, presence of PFAM domains, signal peptides, GPI-anchor propeptides, transmembrane and coiled-coil segments. Furthermore, full-length variants can be now specifically selected based on the annotation of CAGE-tags and polyA signal and/or polyA sites, marking transcription initiation and termination sites, respectively. The retrieval can be carried out at gene, transcript, exon, protein or splice site level allowing the selection of data sets fulfilling one or more features settled by the user.

This content is being maintained by Graziano Pesole.

NAR Database Issue 2011
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tagsalternative splicing exons genetic databases genetic variation humans messenger rna protein isoforms protein sequence analysis proteins

GlyprotTool Content

http://www.glycosciences.de/modeling/glyprot/php/main.php

Other Molecules > Carbohydrates
Protein > 3-D Structural Features

Glyprot is a tool for predicting and modelling all potential N-glycosylation sites in a given 3D structure.

This content is being maintained by luetteke.

NAR Web Server Issue 2005
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tagscomputational biology glycoproteins glycosylation humans molecular models protein conformation protein isoforms

iRefIndexDatabase Content

http://irefindex.uio.no/wiki/iRefIndex

Protein > Interactions, Pathways, Enzymes

iRefIndex provides an index of protein interactions available in a number of primary interaction databases including BIND, BioGRID, CORUM, DIP, HPRD, IntAct, MINT, MPact, MPPI and OPHID. This index allows the user to search for a protein and retrieve a non-redundant list of interactors for that protein.

This content is being maintained by ian.donaldson.

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tagsamino acid sequence analysis of variance animals computational biology data compression data display database management systems humans neural networks (computer) protein databases protein interaction domains and motifs protein interaction mapping protein isoforms proteins proteome proteomics

LOCATEDatabase Content

http://locate.imb.uq.edu.au/

Model Organisms > Mouse and Rat
Protein > Localization and Targeting

LOCATE is a curated database that houses data describing the membrane organization and subcellular localization of mouse proteins.

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tagsanimals membrane proteins mice protein databases protein isoforms proteome

The Protein OntologyDatabase Content

http://pir.georgetown.edu/pro

Protein > Databases

The Protein Ontology (PRO) provides a formal, logically-based classification of specific protein classes including structured representations of protein isoforms, variants and modified forms. PRO now includes representations of protein complexes. The PRO Consortium works in concert with the developers of other biomedical ontologies and protein knowledge bases to provide the ability to formally organize and integrate representations of precise protein forms so as to enhance accessibility to results of protein research.

NAR Database Issue 2011
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tagsanimals controlled vocabulary escherichia coli proteins humans mice multiprotein complexes protein databases protein isoforms proteins

Universal Protein Resource (UniProt)Database Content

http://www.uniprot.org

Protein > Databases

Universal Protein Resource (UniProt) maintains a stable, comprehensive, fully classified, richly and accurately annotated protein sequence knowledgebase, with extensive cross-references and querying interfaces freely accessible to the scientific community. UniProt is comprised of four major components, each optimized for different uses: the UniProt Archive, the UniProt Knowledgebase, the UniProt Reference Clusters and the UniProt Metagenomic and Environmental Sequence Database.

NAR Database Issue 2010NAR Database Issue 2011
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tagsalgorithms amino acid sequence animals computational biology europe fungal genome human genome humans nucleic acid databases protein databases protein isoforms protein sequence analysis proteins proteome proteomics systems integration viral genome

UTRdb/UTRsiteDatabase Content

http://utrdb.ba.itb.cnr.it/

DNA > Databases

UTRdb is a curated database of 5' and 3' untranslated sequences of eukaryotic mRNAs, derived from several sources of primary data. Experimentally validated functional motifs are annotated and also collated as the UTRsite database where more specific information on the functional motifs and cross-links to interacting regulatory protein are provided. UTR entries have been organized in a gene-centric structure to better visualize and retrieve 5' and 3'UTR variants generated by alternative initiation and termination of transcription and alternative splicing. Experimentally validated miRNA targets and conserved sequence elements are also annotated.

NAR Database Issue 2010
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tags3' untranslated regions 5' untranslated regions algorithms animals computational biology genetic databases humans nucleic acid databases plant genome protein databases protein isoforms