>
Tag
> Links tagged with 'nucleic acid sequence homology'

Links tagged with 'nucleic acid sequence homology'

RSS FeedCompact ViewList as XMLList as JSON

Found 60 links

Displaying 15 links

AGenDATool Content

http://bibiserv.techfak.uni-bielefeld.de/agenda/

DNA > Gene Prediction
Sequence Comparison > Analysis of Aligned Sequences

AGenDA is a web tool that compares the genomic sequences from evolutionarily related organisms in order to make gene predictions. It takes pairs of genomic sequences as input, aligns the sequences, and makes predictions based on splice signals, start and stop codons, and areas of conserved sequence.

NAR Web Server Issue 2004
downloadDownload as XMLDownload as JSON
user feedback
0
No votes yet
tagsanimals base sequence conserved sequence dna footprinting dna sequence analysis genes genomics humans mice nucleic acid sequence homology phylogeny rna splicing sequence alignment

ALGGENTool Content

http://alggen.lsi.upc.es/

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
Expression > cDNA, EST, SAGE
Sequence Comparison > Alignment Editing and Visualization
Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Multiple Sequence Alignments

ALLGEN server provides various tools for multiple sequence alignments, clustering, and assembly of ESTs. It also includes search tools for transcription factor binding sites (TFBS), repeated patterns, and transposons.

NAR Web Server Issue 2003
downloadDownload as XMLDownload as JSON
user feedback
0
No votes yet
tagsalgorithms animals binding sites chickens chromosome mapping computational biology conserved sequence dna dna sequence analysis gene expression profiling genetic promoter regions genome genomics humans mice nucleic acid conformation nucleic acid databases nucleic acid regulatory sequences nucleic acid repetitive sequences nucleic acid sequence homology rats sequence alignment software design species specificity transcription factors x-ray crystallography

BioconductorTool Content

http://www.bioconductor.org/

Computer Related > Bio-* Programming Tools
Computer Related > Math and Statistics
Expression > Transcript Expression Analysis

Bioconductor is an open source and open development software project that aims to provide access to a wide range of powerful statistical and graphical methods for the analysis of genomic data.

downloadDownload as XMLDownload as JSON
user feedback
0
No votes yet
tagsalgorithms biological models computational biology computer simulation database management systems dna probes dna sequence analysis gene expression profiling gene expression regulation information dissemination nucleic acid sequence homology oligonucleotide array sequence analysis reproducibility of results sequence alignment signal transduction transcription factors

BLASTTool Content

http://www.ncbi.nlm.nih.gov/BLAST/

DNA > Gene Prediction
DNA > Sequence Retrieval and Submission
Protein > Sequence Retrieval
RNA > Sequence Retrieval
Sequence Comparison > Similarity Searching

Basic Local Alignment Search Tool (BLAST) finds regions of local similarity between sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches. BLAST can be used to infer functional and evolutionary relationships between sequences as well as help identify members of gene families.

NAR Web Server Issue 2004NAR Web Server Issue 2006NAR Web Server Issue 2008
downloadDownload as XMLDownload as JSON
user feedback
0
No votes yet
tagsalgorithms amino acid sequence base sequence factual databases genetic databases genome humans mutation national library of medicine (u.s.) nucleic acid databases nucleic acid sequence homology nucleotides protein databases protein sequence analysis sensitivity and specificity sequence alignment sequence analysis systems integration united states
setsNational Center for Biotechnology Information (NCBI)

BLASTOTool Content

http://oxytricha.princeton.edu/BlastO/index.html

DNA > Phylogeny Reconstruction
Protein > Phylogeny Reconstruction
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Similarity Searching

BLASTO (BLAST on Orthologous groups) is a modified BLAST tool for searching orthologous group data. It treats each orthologous group as a unit and outputs a ranked list of orthologous groups instead of single sequences.

NAR Web Server Issue 2007
downloadDownload as XMLDownload as JSON
user feedback
0
No votes yet
tagsalgorithms animals automated pattern recognition computational biology genetic databases genome genomics humans nucleic acid sequence homology phylogeny species specificity

CARNACTool Content

http://bioinfo.lifl.fr/carnac

RNA > Structure Prediction, Visualization, and Design

Server which predicts conserved secondary structure elements of homologous RNAs. The input of a set of RNA sequences are not required to be previously aligned.

NAR Web Server Issue 2004
downloadDownload as XMLDownload as JSON
user feedback
0
No votes yet
tagsalgorithms catalytic rna cytochromes endoribonucleases enterovirus genetic models messenger rna molecular sequence data nucleic acid conformation nucleic acid databases nucleic acid sequence homology ribonuclease p ribosomal rna rna rna sequence analysis sequence alignment statistical models telomerase viral rna

CentroidHomfold-LASTTool Content

http://www.ncrna.org/centroidhomfold/

RNA > Structure Prediction, Visualization, and Design

CentroidHomfold-LAST predicts the secondary structure of an RNA sequence using automatically collected homologous sequences.

NAR Web Server Issue 2011
downloadDownload as XMLDownload as JSON
user feedback
0
No votes yet
tagsnucleic acid conformation nucleic acid sequence homology rna rna sequence analysis

ClustalXTool Content

http://www.clustal.org/clustal2/

Sequence Comparison > Multiple Sequence Alignments

Clustal X is a version of the Clustal W multiple sequence alignment program with a graphical interface. The display colours allow conserved features to be highlighted for easy viewing in the alignment. It is available for several platforms, including Windows, Macintosh PowerMac, Linux and Solaris.

downloadDownload as XMLDownload as JSON
user feedback
0
No votes yet
tagsalgorithms amino acid sequence animals data display humans molecular sequence data nucleic acid sequence homology nucleic acids phylogeny protein sequence analysis sequence alignment sequence analysis transcription factor tfiib transcription factors

CONREALTool Content

http://conreal.niob.knaw.nl/

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation

CONREAL (Conserved Regulatory Elements Anchored Alignment) allows identification of transcription factor binding sites (TFBS) that are conserved between two orthologous promoter sequences.

NAR Web Server Issue 2005
downloadDownload as XMLDownload as JSON
user feedback
0
No votes yet
tagsalgorithms animals base sequence binding sites conserved sequence dna footprinting dna sequence analysis dna-binding proteins gene expression regulation genetic promoter regions hepatocyte nuclear factor 3-beta humans mice nuclear proteins nucleic acid regulatory sequences nucleic acid sequence homology phylogeny rats sequence alignment takifugu transcription factors zebrafish

cpnDBDatabase Content

http://www.cpndb.ca/cpnDB/home.php

DNA > Phylogeny Reconstruction
Protein > Phylogeny Reconstruction
Protein > Sequence Data
Protein > Sequence Retrieval

cpnDB is a curated collection of chaperonin sequence data collected from public databases or generated by a network of collaborators exploiting the cpn60 target in clinical, phylogenetic and microbial ecology studies. The database contains all available sequences for both group I and group II chaperonins. cpnDB is built and maintained with open source tools.

downloadDownload as XMLDownload as JSON
user feedback
0
No votes yet
tagsanimals bacteria base sequence chaperonin 60 computational biology genetic databases molecular sequence data nucleic acid sequence homology

ERPINTool Content

http://tagc.univ-mrs.fr/erpin/

RNA > Motifs
RNA > Structure Prediction, Visualization, and Design

ERPIN (Easy RNA Profile IdentificatioN) takes as input an RNA sequence alignment and secondary structure annotation and will identify a wide variety of known RNA motifs (such as tRNAs, 5S rRNAs, SRP RNA, C/D box snoRNAs, hammerhead motifs, miRNAs and others) in your sequence(s) of interest. Also contains tool for drawing secondary structure of motifs.

NAR Web Server Issue 2004
downloadDownload as XMLDownload as JSON
user feedback
0
No votes yet
tagsalgorithms base sequence computational biology conserved sequence gene expression regulation iron nucleic acid conformation nucleic acid sequence homology response elements ribonucleic acid regulatory sequences ribosomal rna rna rna sequence analysis selenocysteine sensitivity and specificity sequence alignment transfer rna

EUGENE'HOMTool Content

http://genopole.toulouse.inra.fr/bioinfo/eugene/EuGeneHom/cgi-bin/EuGeneHom.pl

DNA > Annotations
DNA > Gene Prediction
Model Organisms > Plants

EUGENE'HOM is a gene prediction software for eukaryotic organisms based on comparative analysis. The data is currently tuned for plant sequences of up to 400kb.

NAR Web Server Issue 2003
downloadDownload as XMLDownload as JSON
user feedback
0
No votes yet
tagsalgorithms complementary dna dna sequence analysis eukaryotic cells genes genome initiator codon nucleic acid sequence homology plant dna rna splice sites

FASTA ProgramsTool Content

http://fasta.bioch.virginia.edu/

Sequence Comparison > Similarity Searching

Sequence retrieval and comparison tools.

downloadDownload as XMLDownload as JSON
user feedback
0
No votes yet
tagsadrenergic receptors algorithms amino acid sequence animals antigen receptors base sequence dna eye proteins gene library globins humans information systems molecular sequence data nucleic acid sequence homology peptides proteins rod opsins transforming growth factors

FeatureScanTool Content

http://gnaweb.gbf.de/cgi-bin/FeatureScan/FeatureScan.pl

DNA > Structure and Sequence Feature Detection
Sequence Comparison > Similarity Searching

FeatureScan searches for sequence similarity by comparing physico-chemical properties of DNA such as charge, melting enthalpy, conformational parameters, etc.

NAR Web Server Issue 2006
downloadDownload as XMLDownload as JSON
user feedback
0
No votes yet
tagsanimals automated pattern recognition bacterial dna bacterial genes dna dna sequence analysis escherichia coli genetic models genetic promoter regions genomics humans mice nucleic acid sequence homology rats sequence alignment thermodynamics

FOLDALIGNTool Content

http://foldalign.ku.dk

RNA > Motifs
RNA > Structure Prediction, Visualization, and Design

FOLDALIGN is an algorithm for local simultaneous folding and aligning two or more RNA sequences.

NAR Web Server Issue 2005
downloadDownload as XMLDownload as JSON
user feedback
0
No votes yet
tagsalgorithms conserved sequence nucleic acid conformation nucleic acid sequence homology rna rna sequence analysis sequence alignment untranslated rna