| BLAST-2 |
Produces the alignment of two given sequences using BLAST engine for local alignment |
| Pairwise FLAG |
Performs local alignment for two different DNA sequences |
| SCAN2 |
Alignment of genome length DNAs |
| Advanced PipMaker |
Aligns two DNA sequences |
| CoreGenes |
Determines the core set of genes in a maximum of five small genomes |
| ALIGN Query |
Compares two sequences |
| LALIGN |
Finds multiple matching subsegments in two sequences |
| ClustalW |
Multiple Sequence Alignment |
| DbClustal |
Aligns sequences from a BlastP database search with one query sequence |
| MultAlin |
Multiple sequence alignment |
| Multiple Alignment |
This service also provides phylogenetic analysis of the data |
| DiAlign |
DIALIGN constructs pairwise and multiple alignments by comparing whole segments of the sequences |
| BOXSHADE |
Accepts a wide variety of file formats and allows the requester considerable flexibility in defining the output appearance |
| CINEMA |
Colour INteractive Editor for Multiple Alignments for DNA and proteins |
| Multiple Align Show |
accepts a group of aligned sequences (in FASTA or GDE format) and formats the alignment to your specifications |
| Cister |
Cis-element Cluster Finder |
| CONPRO |
CONsensus PROmoter predictor |
| Dragon |
Drogon Promoter finder |
| MatInspector |
Detection of transciption factor binding sites |
| Promotor Scan |
Predicts Promoter regions based on scoring homologies with putative eukaryotic Pol II promoter sequences |
| SignalScan |
Find and list homologies of published signal sequences with the input DNA sequence |
| TATA prediction |
Predict TATA signal in eukaryotic genes |
| TESS |
Transcription element search system |
| Tfsearch |
Searching Transcription Factor Binding Sites |
| Promoter Inspector |
Prediction of promoter regions in mammalian genomic sequences |
| Promotor Prediction |
Neural network promoter prediction |
| ORF Finder |
Search for open reading frame, at NCBI |
| FGENEH |
Splice sites, protein coding exons and Gene models construction, promotor and poly-A search |
| Gene Finder |
Predict protein coding exons in genomic DNA |
| GeneID |
Gene identification and structure prediction |
| GeneMark |
Inhomogeneous Markov model approach combined with training datasets to predict genes |
| GeneParser2 |
Identification of protein coding regions |
| Generation |
Microbial gene prediction |
| Genie |
Gene finder based on hidden Markov models |
| GenLang |
Linguistics based method to find genes |
| GenScan |
Identification of gene structures in genomic DNA |
| GenViewer |
Predicting and analysis of protien-coding gene structures |
| Glimmer |
A system for finding genes in microbial DNA |
| Grail |
DNA sequence analysis tool |
| HMMGene |
Prediction of vertebrate and C. elegans genes |
| NetGene2 |
Neural network predictions of splice sites |
| Procrustus |
Gene recognition via spliced alignment |
| SpliceSite Prediction |
Splice site prediction by neural network |
| Wise2 |
Intelligent algorithm for DNA searches |
| WebGene |
Several tools for prediction and analysis of protein coding gene structures |
| Xgrail |
Find exons and other features |
| Primer3 |
A very powerful PCR primer design program |
| GeneFisher |
A very good site allowing great control over primer design |
| CODEHOP |
PCR primers designed from protein multiple sequence alignments |
| PRIDE |
Primer design for large-scale projects in sequencing, PCR, and DNA array design |
| DoPrimer |
Not abailable |
| Oligo Analyzer |
Primer selection program by IDT |
| Poland |
Calculate the thermal denaturation profile of double-stranded RNA, DNA or RNA/DNA-hybrids based on sequence input and parameter settings in this form. |
| DAN |
Calculates DNA RNA/DNA melting temperature (EMBOSS) |
| Biopolymer Calculator |
Calculates molecular weight, melting temperature |
| Oligonucleotide Properties Calculator |
Oligonucleotide Properties Calculator |
| Nucleic Acid Sequence Massager |
Format and manipulating nucleic acid sequences, reverse, complement, etc. |
| Readseq |
Biosequence conversion tool |
| VecScreen |
Screens your DNA sequence for potential vector sequence |
| WORDCOUNT |
Counts words of a specified size in a DNA sequence (EMBOSS) |
| Cumulative GC-Skew |
Take a DNA sequence and calculates %GC percentage, GC-skew or cumulative GC-skew using a user defined window |
| CAP3 |
Contig Assembly Program |
| ERR_WISE |
Detection of Frameshift Sequencing Error |
| Wise2: DNA vs Protein |
Compares a protein sequence to a genomic DNA sequence, allowing for introns and frameshifting errors |
| CloneIt |
An online program finding sub-cloning strategies,in-frame deletions and frameshifts using restriction enzymes and DNA polymerases |
| Physical Mapping Calculator |
Shows how the library redundancy and %% of genome covered depends on the number of clones in a library |
| Webcutter |
Restriction endonuclease digestion |
| Restriction Site Analysis |
Provides one with considerable choice of enzymes and output format. |
| Reverse Complement |
Converts a DNA sequence into its reverse, complement, or reverse-complement |
| Phred/Phrap/Consed |
Phres: Reads sequence trace data, make base calls and assigns quality values. Phrap: Program to assemble DNA sequences |
| Improbizer |
Searches for motifs in DNA or RNA sequences that occur with improbable frequency |
| Filter DNA |
Removes non-DNA characters from text |
| GenBank to Fasta |
Convert GenBank input to fasta format |
| DNA Analyzer |
Multipurpose DNA analyzer |
| Nucleic acid calculator |
From A260nm calculate DNA, RNA and oligonucleotide concentrations online |
| Reverse Translate a Protein |
Enter a protein sequence and obtain its reverse translation for use in design of degenerate oligonucleotides. The program uses the standard genetic code and does not consider differences in codon usage |
| Backtranslation |
Provides one with a wealth of options include organism-specific codon usage |
| Reverse Translator |
Changing a specific amino acid into another |
| ExPASy Translate tool |
Useful if you have a gene which begins with an alternative start codon. |
| Third Position GC Skew Display |
Predicts genes by comparing possible open reading frames (variety of initiation codon options) to a third position GC plot. This tool is apparently most effective for genomes with a high G+C content |
| Reverse Translate |
Accepts protein sequence and uses a codon usage table to generate a graph that can be used to find regions of minimal degeneracy at the nucleotide level |
| Structure Prediction Meta-server |
Runs PDB-Blast, ORFeus, FFAS, 3D-PSSM, GenTHREADER, mGenTHREADER, INBGU, ShotGun-INBGU, Sam-T99, FUGUE2, SUPERFAMILY, Jpred2, and PsiPred. |
| VAST |
Structure-structure similiarity search |
| PSA |
The Protein Sequence Analysis (PSA) server predicts probable secondary structures and folding classes for a given amino acid sequence |
| PredictProtein |
PredictProtein is a service for sequence analysis, and structure prediction |
| JPred |
A consensus method for protein secondary structure prediction |
| NPSA |
Provides different methods for protein secondary structure prediction |
| Folding@home |
Protein folding |
| Multicoil |
Predict coiled coil structures |
| MultPredict |
Secondary Structure of Multiply Aligned Sequences |
| NNPredict |
Protein secondary structure prediction |
| Predator |
Secondary structure prediction |
| PredictProtein |
Sequence analysis and structure prediction |
| SSCP |
Predicts helix, strand, and coil for a given protein |
| SSPSI |
Threading program for protein secondary structure |
| ToPLign |
Alignment and structure prediction by threading |
| SOSUI |
Secondary structure prediction of membrane proteins |
| TMpred |
Prediction of Trans-membrane Regions and Orientation |
| TMHMM |
Prediction of transmembrane helices in proteins |
| DAS |
Transmembrane Prediction Server |
| TopPred |
Topology prediction of membrane proteins |
| SignalP |
Protein signal prediction |
| TargetP |
Prediction of subcellular location |
| PSORT |
A series of programs for the prediction of protein localization sites in cells. Choose programs specific for for animal, yeast, plant or bacterial proteins |
| SIGFIND2 |
Predicts signal peptides at the start of eukaryotic protein sequences or searches open reading frames with a potential signal peptide coded in nucleotide sequences |
| ProtComp |
Can be used to predict the subcellular localization for animal/fungal and plant proteins |
| SWEET |
Constructs 3D model of saccharides from their sequences using standard nomenclature |
| 3D-PSSM |
Protein Fold Recognition using 1D and 3D Sequence Profiles coupled with Secondary Structure and Solvation Potential Information |
| SWISS-MODEL |
An automated comparative protein modelling server |
| SDSC1 |
SDSC Protein Structure Homology Modeling |
| 3D-JIGSAW |
Builds three-dimensional models for proteins based on homologues of known structure |
| WHAT IF |
Offers one a large number of tools for examining PDB files |
| PDB2MultiGIF |
Takes the 3D structure and generates an animated image which can be displayed using any browser |
| FUGUE |
Sequence-structure homology recognition |
| Proinformatix |
Modeling oligopeptides for energetically minimized structures |
| Blocks |
Search DNA or protein sequence against a Blocks database |
| DomainParser |
A protein domain partition program |
| PatternSearch |
Search a pattern against protein databases |
| ProfileScan |
Search for a protein profile |
| MEME |
Motif discovery tool |
| MAST |
Motif alignment and search tool |
| VAST |
Comparison of 3-dimensional protein structures |
| SMART |
Simple modular architecture research tool |
| Prosite |
Search a motif against Prosite database |
| Pfam |
Classification of protein families |
| Motif |
Search a protein motif in Prosite pattern or profile, Blocks, ProDom, Prints, Pfam databases or DNA motif in Transfac database or a user defined database |
| PRINTS |
Search against a protein finger print database |
| ProDom |
The protein domain database |
| PatScan |
Search a pattern in protein/nucleic acid database |
| InterProScan |
Includes Pfam, Prosite and Prints |
| PANAL |
Searches Prosite patterns & profiles, BLOCKS, PRINTS and Pfam |
| eMATRIX |
Includes these sites and PRODOM, and DOMO databases. |
| CDD (Conserved Domain Databases) |
Includes Smart and Pfam and is invoked when one uses BLASTP |
| Pfam HMM |
Analyze a query sequence by searching Pfam HMMs |
|
Scan a protein sequence for the occurrence of patterns and profiles stored in the PROSITE database, or to search protein databases with a user-entered pattern |
| fingerPRINTScan |
Consult PRINTS for further information on the motifs |
| One to three |
Convert single letter code to three letter code |
| Three to one |
Convert three letter code to single letter code |
| ProtScale |
Allows you to compute and represent the profile produced by any amino acid scale on a selected protein. |
| SAPS |
Statistical Analysis of Protein Sequences |
| ProtParam tool |
Allows the computation of various physical and chemical parameters for a given protein |
| Compute pI/Mw tool |
Allows the computation of the theoretical pI (isoelectric point) and Mw (molecular weight) |
| PEPSTATS |
Protein statistics |
| CYSREDOX |
Calculate the redox state of cysteine residues in proteins |
| CYSPRED |
Predictor of bonding state of cysteines in proteins |
| Cutter |
Cutter is a program that allows to generate peptide fragments by the enzymatic or chemical cleavage of a protein sequence |
| FLICKER |
Comparing images, such as two 2-D gels from different Internet sources on your Web browser |
| K2d |
Prediction of percentages of protein secondary structure from CD spectra |
| MOWSE |
Molecular weight search against a peptide mass database |