Match: All Any Boolean

Category bioinformatik.de / Software / Online Tools /

Directories (6)

Protein Analysis (7)

AutoPrime - Primers for expressed sequences. AutoPrime allows the effortless design of primers for Real-Time PCR. It employs the Primer3 software and sequence information from the Ensembl database to automate the process to the highest degree.
http://www.autoprime.de/

BCM Search Launcher - Run BLAST searches, gene prediction programs, protein secondary structure prediction, and multiple alignments in batch mode.
http://www.hgsc.bcm.tmc.edu/SearchLauncher/

Bioinformatic Workflow Builder Interface (BioWBI) is an easy-to-use, Web-based working environment from which a Life Sciences researcher and/or a research community can build and execute bioinformatic workflows and share their analysis processes.
http://www.alphaworks.ibm.com/tech/biowbi

BLAST - NCBI's sequence similarity search tool designed to support analysis of nucleotide and protein databases.
http://www.ncbi.nlm.nih.gov/BLAST/

CDD - NCBI Conserved Domain Database Search.
http://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml

CloneIt! - An online Version of the CloneIt program finding cloning strategies using restriction enzymes & DNA polymerases.
http://topaze.jouy.inra.fr/cgi-bin/CloneIt/CloneIt

CONSENSUS: Identification of consensus patterns in unaligned DNA and protein sequences (Hertz & Stormo).
http://bioweb.pasteur.fr/seqanal/interfaces/consensus-simple.html

ConStruct is a tool for prediction of conserved secondary structure of a set of homologous single-stranded RNA.
http://www.biophys.uni-duesseldorf.de/local/ConStruct.html

Database Searching, Browsing and Analysis Tools - EMBL Outstation, Hinxton.
http://www2.ebi.ac.uk

ESTblast - A tool for contig building with Expressed Sequence Tags.
http://www.hgmp.mrc.ac.uk/ESTBlast/

ESTScan is a program that can detect coding regions in DNA sequences, even if they are of low quality. ESTScan will also detect and correct sequencing errors that lead to frameshifts.
http://www.ch.embnet.org/software/ESTScan.html

FastM - definition of organizational patterns in DNA sequences. Search for two distance-correlated transcription factor binding sites.
http://www.gsf.de/cgi-bin/fastm.pl

GenLang is a syntactic pattern recognition system, which uses the tools and techniques of computational linguistics to find genes and other higher-order features in biological sequence data.
http://www.cbil.upenn.edu/genlang/genlang_home.html

HMM-based Sequence Query, SAM-T99
http://www.cse.ucsc.edu/research/compbio/HMM-apps/T99-query.html

HMMTOP: Prediction of transmembrane helices and topology of proteins.
http://www.enzim.hu/hmmtop/

iMolTalk accepts PDB code or PDB formatted model files and provides computation of: structural alignment, residue contacts, determination of protein-protein interfaces, contact maps and more.
http://i.moltalk.org/

kPROT server: A sequence-derived scale for membrane protein structure prediction.
http://bioinfo.weizmann.ac.il/kPROT/

miniPEDANT displays primary information such as statistical evaluation of protein properties, best BLAST hits, multiple alignment to homologous sequences, presence of sequences domain, domain patterns etc.
http://mips.gsf.de/proj/hnb/minipedant/

Molphy (J. Adachi & M. Hasegawa): ProtML, NucML and NJDist
http://bioweb.pasteur.fr/seqanal/interfaces/molphy.html

PAT, for Protein Analysis Toolkit, is an integrated biocomputing server. This server facilitates the combination of different processing tools for complex protein analyses and permits the automation of repetitive tasks.
http://pat.cbs.cnrs.fr

PeptideMass cleaves one or more protein sequences from the SWISS-PROT and/or TrEMBL databases or auser-entered protein sequence with a chosen enzyme, and computes the masses of the generated peptides.
http://www.expasy.ch/tools/peptide-mass.html

Phylodendron - Phylogenetic tree printer.
http://iubio.bio.indiana.edu/treeapp/treeprint-form.html

Phylogenetic tree prediction, GeneBee services
http://www.genebee.msu.su/services/phtree_reduced.html

Plot the Hydropathic Profile of a Protein.
http://bioinformatics.weizmann.ac.il/hydroph/plot_hydroph.html

PREDATOR - Protein secondary structure prediction from a single sequence or a set of sequences
http://bioweb.pasteur.fr/seqanal/interfaces/predator-simple.html

ProtParam is a tool which allows the computation of various physical and chemical parameters for a given protein stored in SWISS-PROT or TrEMBL or for a user entered sequence.
http://www.expasy.ch/tools/protparam.html

ProtScale allows you to compute and represent the profile produced by any amino acid scale on a selected protein.
http://www.expasy.ch/cgi-bin/protscale.pl

Pyramids: A pyramidal analysis tool for sequence clustering
http://bioweb.pasteur.fr/seqanal/interfaces/pyramids-simple.html

RepeatMasker screens DNA sequences in fasta format against a library of repetitive elements and returns a masked query sequence ready for database searches as well as a table annotating the masked regions.
http://ftp.genome.washington.edu/cgi-bin/RepeatMasker

Restriction Enzyme analysis (Mangalam)
http://bioweb.pasteur.fr/seqanal/interfaces/tacg.html

RNA secondary structure prediction, Genebee services
http://www.genebee.msu.su/services/rna2_reduced.html

Sequence Analysis Tools at NIH
http://molbio.info.nih.gov/molbio/analysis.html

SeWeR - Sequence analysis using Web Resources.
http://www.bioinformatics.org/sewer/

SOSUI - Classification and Secondary Structure Prediction of Membrane Proteins .
http://sosui.proteome.bio.tuat.ac.jp/sosuiframe0.html

SplitsTree uses the split decomposition method to analyze and visualize distance data, especially extracted from biological sequences.
http://bibiserv.techfak.uni-bielefeld.de/splits/

STRIDE - Protein secondary structure assignment from atomic coordinates
http://bioweb.pasteur.fr/seqanal/interfaces/stride-simple.html

Tandem repeats finder: a program to analyze DNA sequences.
http://c3.biomath.mssm.edu/trf.html

Teiresias-based gene expression analysis.
http://cbcsrv.watson.ibm.com/Tgea.html

Teiresias-based pattern discovery for unaligned sequences (proteins and DNA).
http://cbcsrv.watson.ibm.com/Tspd.html

Teiresias-based text mining for word and letter ASCII streams in free format.
http://cbcsrv.watson.ibm.com/Ttwpd.html

The Gene2EST BLAST Server.
http://woody.embl-heidelberg.de/gene2est/

The Poland server will calculate the thermal denaturation profile of double-stranded RNA, DNA or RNA/DNA-hybrids.
http://www.biophys.uni-duesseldorf.de/local/POLAND/poland.html

The PSIPRED protein structure prediction server allows you to submit a protein sequence, perform a prediction of your choice and receive the results of the prediction via E-mail.
http://globin.bio.warwick.ac.uk/psipred/

Tm Determination - Determines Tm for a given sequence at a particular DNA concentration.
http://alces.med.umn.edu/rawtm.html

TMHMM - Prediction of transmembrane helices in proteins.
http://www.cbs.dtu.dk/services/TMHMM-1.0/

TRADAT - TRAnscription Databases and Analysis Tools.
http://www.itba.mi.cnr.it/tradat/

WEBGENE - Tools for prediction and analysis of protein-coind gene structure.
http://www.itba.mi.cnr.it/webgene/

Webinterface for Phylip programs.
http://bioweb.pasteur.fr/seqanal/phylogeny/phylip-uk.html