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Links tagged with 'prokaryotic cells'

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iCRTool Content

http://210.212.215.199/icr/index.html

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
Protein > Interactions, Pathways, Enzymes

Identify Conserved targets of a Regulon (iCR) predicts regulatory binding sites based on conservation across multiple species. The user provides an ungapped multiple sequence alignment representing the regulatory binding site. iCR reports back with predicted binding sites that are conserved and highlights the downstream co-regulated genes.

NAR Web Server Issue 2006
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tags5' flanking region bacterial genome bacterial proteins binding sites dna-binding proteins genomics mycobacterium tuberculosis nucleic acid regulatory sequences operon prokaryotic cells regulon sequence alignment serine endopeptidases transcription factors transcriptional regulatory elements

ISfinderDatabase Content

http://www-is.biotoul.fr

DNA > Databases

ISfinder is a dedicated insertion sequence (IS) database which assigns names to individual ISs to maintain a coherent nomenclature, an IS repository including >3000 individual ISs from both bacteria and archaea and provides a basis for IS classification. Each IS is indexed in ISfinder with various associated pieces of information (the complete nucleotide sequence, the sequence of the ends and target sites, potential open reading frames, strain of origin, distribution in other strains and available bibliography) and classified into a group or family to provide some insight into its phylogeny. ISfinder also includes extensive background information on ISs and transposons in general. ISbrowser, an extension to the ISfinder platform and a tool, which permits visualization of the position, orientation and distribution of complete and partial ISs in individual prokaryotic genomes.

This content is being maintained by mchandler.

NAR Database Issue 2010
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tagsalgorithms bacterial genome biotechnology computational biology gene expression profiling genetic databases nucleic acid databases phylogeny prokaryotic cells protein databases

LOCtargetTool Content

http://www.rostlab.org/services/LOCtarget/

Protein > Annotation and Function

LOCtarget is a tool for predicting, and a database of pre-computed predictions for, sub-cellular localization of eukaryotic and prokaryotic proteins. Several methods are employed to make the predictions, including text analysis of SWISS-PROT keywords, nuclear localization signals, and the use of neural networks.

NAR Web Server Issue 2004
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tagsamino acid sequence homology eukaryotic cells genetic databases genomics neural networks (computer) nuclear localization signals prokaryotic cells protein sequence analysis protein sorting signals proteins

PredictRegulonTool Content

http://www.cdfd.org.in/predictregulon/

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation

PredictRegulon is a tool that, for a given regulatory protein and prokaryotic genome, predicts binding sites and operons. The user selects a prokaryote genome and provides an ungapped multiple sequence alignment representing the binding site. PredictRegulon reports back with predicted binding sites and downstream co-regulated genes.

NAR Web Server Issue 2004
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tags5' flanking region bacterial genome bacterial proteins binding sites mycobacterium tuberculosis nucleic acid regulatory sequences operon prokaryotic cells regulon sequence alignment serine endopeptidases transcription factors

Ribosomal Database ProjectDatabase Content

http://rdp.cme.msu.edu/

DNA > Phylogeny Reconstruction
Protein > Phylogeny Reconstruction
RNA > Functional RNAs
RNA > Sequence Retrieval

Highly curated database of aligned and annotated rRNA sequences with accompanying phylogenies; data available for download.

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tagsanimals archaea archaeal rna bacteria bacterial rna eukaryotic cells nucleic acid databases phylogeny prokaryotic cells ribosomal rna rna sequence analysis sequence alignment

RNAzTool Content

http://rna.tbi.univie.ac.at/cgi-bin/RNAz.cgi

RNA > Structure Prediction, Visualization, and Design
Sequence Comparison > Analysis of Aligned Sequences

RNAz detects functional RNA secondary structures in multiple sequence alignments based on thermodynamic stability and structural conservation.

NAR Web Server Issue 2007
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tagsalgorithms archaea base sequence computational biology consensus sequence conserved sequence escherichia coli genome molecular evolution molecular sequence data nucleic acid conformation nucleic acid databases nucleic acid sequence homology phylogeny prokaryotic cells ribonucleic acid regulatory sequences ribosomal rna rna rna sequence analysis rna stability sequence alignment thermodynamics untranslated rna

TiCoTool Content

http://tico.gobics.de/

DNA > Gene Prediction
Model Organisms > Microbes

TIS Correction (TiCo) is a tool for improving predictions of prokaryotic Translation Initiation Sites (TIS). TiCo can be used to analyze and reannotate predictions obtained by the program GLIMMER.

NAR Web Server Issue 2006
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tagsalgorithms artificial intelligence automated pattern recognition bacterial genome base sequence cluster analysis dna sequence analysis genomics initiator codon molecular sequence data prokaryotic cells prokaryotic initiation factors protein biosynthesis translational peptide chain initiation