Web Tools

WebGene  
Tools for prediction and analysis of protein-coding gene structure: An integrated computing system for protein-coding gene prediction, Gene structure prediction using information on homologous protein sequence, EST Mapping, CDS prediction based on Silent/Replacement ratio, Repeated elements mapping, CpG islands prediction, Splicing signals prediction, Hamming Clustering Method for Poly-A prediction in Eukaryotic Genes, Hamming Clustering Method for TATA signal prediction in Eukaryotic Genes, A computing system for protein-coding gene prediction.
Submitted: Dec 02, 2000
Neural Network Promoter Prediction  
NNPP is a method that finds eukaryotic and prokaryotic promoters in a DNA sequence. The function of the promoter as a initiator for transcription is one of the most complex processes in molecular biology. It has been shown that multiple functional sites in the primary DNA are involved in the polymerase binding process. These elements, such as the TATA-box and the transcription start site ("Initiator") for eukaryotes, are known to function as binding sites for Polymerase II, transcription factors, and other proteins that are involved in the transcription initiation process. These promoter elements are present in various combinations separated by various distances in the sequence.
Submitted: Dec 02, 2000
Genie: Gene Finder  
Genie is currently a prototype that is only set up to find multi-exon genes, and it tries to find exactly one gene on each strand (forward and reverse) of each sequence submitted. If you give Genie a sequence with more than one gene per strand, it will not give satisfactory results. You may submit multiple sequences (in multiple-FASTA format); Genie will predict a gene separately for each sequence.
Submitted: Dec 02, 2000
NetGene2  
The NetGene2 World Wide Web server is a service producing neural network predictions of splice sites in human, C. elegans and A. thaliana DNA.
Submitted: Dec 02, 2000
GeneWalker  
GeneWalker helps you designing your primers. It is a powerful tool, yet it is based on the philosophy of ease to use. GeneWalker allows you to work with two primer sequences simultaneously. You can also toggle between reversed complementary primer sequences. Basic functions includes calculation of primer secondary structures, primer annealing properties as well as primer dimers. GeneWalker also helps you to easily connect to EMBLs databases.
Submitted: Dec 02, 2000
STRING  
Search for Tandem Repeats IN Genomes.
Submitted: Apr 15, 2003
Transcription Element Search System  
TESS (Transcription Element Search Software) is a set of software for locating and displaying transcription factor binding sites in DNA sequence. TESS uses the Transfac database as its store of transcription factors and their binding sites.
Submitted: Dec 02, 2000
Genscan  
This server provides access to the program Genscan for predicting the locations and exon-intron structures of genes in genomic sequences from a variety of organisms.
Submitted: Dec 02, 2000
HMMgene  
HMMgene is a program for prediction of genes in anonymous DNA, which predicts whole genes, so the predicted exons always splice correctly. It can predict several whole or partial genes in one sequence, so it can be used on whole cosmids or even longer sequences. HMMgene can also be used to predict splice sites and start/stop codons. If some features of a sequence are known, such as hits to ESTs, proteins, or repeat elements, these regions can be locked as coding or non-coding and then the program will find the best gene structure under these constraints.
Submitted: Dec 02, 2000
TreeGen  
Compute phylogenetic trees and 2D optimal placements based on distance matrices and optional variances.
Submitted: Oct 25, 2000
PLACE  
PLACE is a database of motifs found in plant cis-acting regulatory DNA elements, all from previously published reports. It covers vascular plants only. In addition to the motifs originally reported, their variations in other genes or in other plant species reported later are also compiled. The PLACE database also contains a brief description of each motif and relevant literature with PubMed ID numbers. DDBJ/EMBL/GenBank nucleotide sequence databases accession numbers will be also included.
Submitted: Dec 02, 2000
Poland  
The Poland server will calculate the thermal denaturation profile of double-stranded RNA, DNA or RNA/DNA-hybrids based on sequence input and parameter settings in this form. Calculation is based on Poland's algorithm in the implementation described by Steger. Graphics results are directly sent to your WWW client.
Submitted: Dec 02, 2000
Proteome Analysis  
The genome sequencing projects are providing a vast amount of sequence data which remain largely unexploited. With access to whole genome sequences from various organisms and imminent completion of many more, the SWISS-PROT group at EBI has decided to develop a research-oriented initiative in order to utilise all the existing resources and provide comparative analysis of the predicted protein coding sequences of all complete genomes. The two main projects used in this proteome analysis effort, InterPro and CluSTr, are aiming to give a new perspective on domain structure and function, gene duplication and protein families in different genomes.
Submitted: Dec 09, 2000
Ribosomal RNA Mutation Databases  
The 16S Ribosomal RNA Mutation Database (16SMDB) consists of an annotated list of 484 alterations distributed over 157 positions in 16S ribosomal RNA from Escherichia coli. Mutated positions are arranged in order beginning with the 5' end of 16S rRNA and ending with the 3' end. Phenotypes associated with each alteration are briefly described and designated as to whether the phenotypes were detected in vivo or in vitro . Appropriate references are provided for each alteration. The 23S Ribosomal RNA Mutation Database (23SMDB) consists of an annotated list of 418 alterations distributed over 143 positions in 23S ribosomal RNA from Escherichia coli. The expanded versions include data from E.coli and from other organisms; these files are entitled 16SMDBexp and 23SMDBexp, giving a total number of 977 entries in the database: 522 entries for 16S and 455 entries for 23S. Files containing only the data from organisms other than E. coli are entitled 16S-likeMDB and 23S-likeMDB.
Submitted: Dec 02, 2000
FramePlot  
A web-based protein-coding region prediction tool for high GC-content bacteria DNA, such as Streptomyces.
Submitted: Dec 02, 2000
Human Blast Server at Sanger  
Allows the searching of a DNA database containing all human sequence data available from the Sanger Centre.
Submitted: Dec 02, 2000
PipMaker  
PipMaker computes alignments of similar regions in two DNA sequences. The resulting alignments are summarized with a ``percent identity plot'', or ``pip'' for short.
Submitted: Dec 02, 2000



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