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Links tagged with 'statistical data interpretation'

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Found 31 links

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ArrayXPathTool Content

http://www.snubi.org/software/ArrayXPath/

Expression > Transcript Expression Analysis
Protein > Interactions, Pathways, Enzymes

ArrayXPath is a web-based service for matching microarray gene-expression profiles with known biological pathways. Input is a clustered gene-expression profile in a tab-delimited text format. Output includes pathway diagrams.

NAR Web Server Issue 2004NAR Web Server Issue 2005
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tagscluster analysis gene expression profiling genetic databases genetic predisposition to disease medical subject headings oligonucleotide array sequence analysis signal transduction statistical data interpretation systems integration

COMPASSTool Content

http://prodata.swmed.edu/compass/compass.php

Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Similarity Searching

COMPASS (Comparison of Multiple Protein Alignments with Assessment of Statistical Significance) is a tool for detecting remote levels of sequence similarity using profile-based comparison of multiple sequence alignments. Statistics and speed have been improved, and visualization tools introduced.

NAR Web Server Issue 2007NAR Web Server Issue 2009
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tagsamino acid motifs amino acid sequence amino acid sequence homology capsid proteins clathrin computational biology mamastrovirus molecular evolution molecular models molecular sequence data protein conformation protein databases protein structural homology proteins reproducibility of results secondary protein structure sensitivity and specificity sequence alignment statistical data interpretation statistics as topic tertiary protein structure trna methyltransferases

CorGenTool Content

http://corgen.molgen.mpg.de

DNA > Structure and Sequence Feature Detection

CorGenmeasures long-range correlations in DNA sequences and can generate random sequences with the same (or user-specified) correlation and composition parameters.

NAR Web Server Issue 2006
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tagsalgorithms base composition computational biology cytosine dna sequence analysis genomics guanine humans sequence alignment statistical data interpretation

DAVID Bioinformatics ResourcesTool Content

http://david.abcc.ncifcrf.gov/home.jsp

DNA > Annotations
Expression > Gene Regulation
Human Genome > Annotations
Protein > Interactions, Pathways, Enzymes
Sequence Comparison > Comparative Genomics

The Database for Annotation, Visualization and Integrated Discovery (DAVID) provides a comprehensive set of functional annotation tools for investigators to understand biological meaning behind large list of genes.

NAR Web Server Issue 2007
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tagsalgorithms automated pattern recognition computational biology gene expression profiling genetic databases genomics hiv-1 humans macrophages mononuclear leukocytes nucleic acid databases oligonucleotide array sequence analysis statistical data interpretation

DBAliDatabase Content

http://salilab.org/DBAli/

Protein > 3-D Structure Comparison
Protein > Annotation and Function
Protein > Domains and Motifs

DBAli is a database that includes a comprehensive all-against-all comparison of protein structures in the PDB database. Tools associated with the database allow users to mine this protein structure space by establishing relationships between protein structures and their functions.

NAR Web Server Issue 2007
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tagsalgorithms amino acid sequence amino acid sequence homology computational biology molecular sequence data protein conformation protein databases protein sequence analysis proteins pseudomonas aeruginosa sequence alignment software design statistical data interpretation structure-activity relationship

DEEPTool Content

http://www.bioinf.med.uni-goettingen.de/services/deep/

Expression > Gene Regulation
Expression > Transcript Expression Analysis
Expression > cDNA, EST, SAGE
Protein > Interactions, Pathways, Enzymes

DEEP (Differential Expression Effector Prediction) is a tool that can identify effectors of specific expression profiles by combining gene expression data with biological expert knowledge about biomolecular interaction networks (provided by resources like TRANSPATH, for example).

NAR Web Server Issue 2007
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tagsalgorithms animals biological models computational biology computer simulation gene expression profiling genetic models humans phenotype protein interaction mapping signal transduction statistical data interpretation

DHcLTool Content

http://sitron.bccs.uib.no/dhcl/

Protein > Domains and Motifs

DHcL provides analysis of the hierarchy of protein domain structures. DHcL detects closed loops and van der Waals locks, and outputs domain decomposition at different levels of protein domain structure hierarchy.

NAR Web Server Issue 2008
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tagsmolecular models statistical data interpretation tertiary protein structure x-ray crystallography

fastSCOPTool Content

http://gemdock.life.nctu.edu.tw/fastSCOP/

Protein > 3-D Structure Comparison
Protein > Domains and Motifs
Sequence Comparison > Similarity Searching

fastSCOP identifies structural domains and determines evolutionary superfamilies of a query protein structure using 3D-BLAST to scan SCOP and MAMMOTH to create a structural alignment for refining domain boundaries.

NAR Web Server Issue 2007
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tagsamino acid sequence amino acid sequence homology computational biology molecular evolution molecular models molecular sequence data protein conformation protein databases protein sequence analysis protein structural homology proteins statistical data interpretation tertiary protein structure

g:ProfilerTool Content

http://biit.cs.ut.ee/gprofiler/

DNA > Annotations
DNA > Sequence Polymorphisms
Expression > Gene Regulation
Expression > Transcript Expression Analysis
Protein > Domains and Motifs
Protein > Interactions, Pathways, Enzymes

g:Profiler is a set of tools for functional annotation of gene lists that includes: g:GOSt, which retrieves the most significant Gene Ontology (GO) terms, KEGG and REACTOME pathways, and TRANSFAC motifs; g:Convert, for conversion between gene or protein names/IDs; g:Orth, for retrieving orthologs; and, g:Sorter, which searches for similar expression profiles. Functional analysis of SNPs and other DNA polymorphisms is also supported, as is enrichment analysis.

NAR Web Server Issue 2007NAR Web Server Issue 2011
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tagsalgorithms animals computational biology dna gene expression profiling genomics humans messenger rna oligonucleotide array sequence analysis statistical data interpretation

GDAPTool Content

http://www.doe-mbi.ucla.edu/Services/GDAP

Protein > Biochemical Features
Protein > Sequence Features

The Genomic Disulfide Analysis Program (GDAP) predicts disulfide bonds for a user-supplied protein sequence. GDAP also provides access to pre-computed predictions of disulfide bonds for over 100 microbial genomes.

NAR Web Server Issue 2004
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tagsarchaeal genome archaeal proteins bacterial genome bacterial proteins cysteine disulfides protein sequence analysis statistical data interpretation

GFINDerTool Content

http://www.medinfopoli.polimi.it/GFINDer/

Expression > Transcript Expression Analysis

Genome Functional INtegrated Discoverer (GFINDer) takes a list of gene/clone IDs with classification information as input, and allows the user to characterize the different gene classes in the list using annotations of various types from several different sources.

NAR Web Server Issue 2004NAR Web Server Issue 2005
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tagscomputational biology controlled vocabulary gene expression profiling genetic databases genomics humans inborn genetic diseases oligonucleotide array sequence analysis phenotype proteins statistical data interpretation systems integration

JProGOTool Content

http://www.jprogo.de/index.jsp

Expression > Transcript Expression Analysis
Model Organisms > Microbes

JProGO is a tool for the functional interpretation of prokaryotic microarray data using Gene Ontology information.

NAR Web Server Issue 2006
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tagsarchaea archaeal genes bacteria bacterial genes controlled vocabulary gene expression profiling oligonucleotide array sequence analysis statistical data interpretation

KOBASTool Content

http://kobas.cbi.pku.edu.cn

DNA > Annotations
Human Genome > Databases
Protein > Interactions, Pathways, Enzymes

KEGG Orthology-Based Annotation System (KOBAS) annotates sequences with KEGG Orthology terms and identifies the frequently occurring (or significantly enriched) pathways among the queried sequences compared against a background distribution. 5 pathway databases are used (KEGG Pathway, PID, BioCyc, Reactome, Panther) and 5 human databases (OMIM, KEGG Disease, FunDO, GAD, NHGRI GWAS).

NAR Web Server Issue 2006NAR Web Server Issue 2011
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tagsalzheimer disease artificial intelligence biological models chromosome mapping controlled vocabulary database management systems documentation genes genetic databases hippocampus natural language processing proteins proteome sequence analysis signal transduction statistical data interpretation up-regulation

MaXIC-QTool Content

http://ms.iis.sinica.edu.tw/MaXIC-Q

Protein > Proteomics

The MaXIC-Q web server performs various quantification analyses on large-scale datasets generated from proteomics studies using isotope labeling. For input MS data, output is given in projected ion mass spectrum and extracted ion chromatograph which can be used to generate other calculations (e.g. ion abundances and peptide-protein ratios.

NAR Web Server Issue 2009
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tagscomputational biology endothelial cells isotope labeling liquid chromatography mass spectrometry nitric acid peptides proteins reproducibility of results statistical data interpretation

MEGATool Content

http://www.megasoftware.net/

DNA > Phylogeny Reconstruction
Protein > Phylogeny Reconstruction

MEGA (Molecular Evolutionary Genetics Analysis) is a software package for phylogenetic analysis with a graphical user interface. It allows viewing and editing of the aligned input sequence data and provides many tools for phylogenetic and statistical analysis of the alignments.

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tagsdna dna sequence analysis genetic databases molecular evolution phylogeny protein sequence analysis proteins sequence alignment statistical data interpretation