Israel Science and Technology Directory

Biomedical : Online Software for Sequence Analysis

Online ToolDescription
* Also see Primer Design Tools
3DNASoftware system for the analysis, rebuilding, and visualization of three-dimensional nucleic-acid-containing structures
AmiGeneAnnotation of Microbial Genes for for automatically identifying the most likely CoDing Sequences (CDSs).
BLAST Search of Nucleotide, Protein and Genome DatabasesCompare your query sequence to the working draft sequence of the human genome or its mRNA and protein products.
Biology WorkBenchProtein tools: structure prediction, blast, multiple sequence alignment, randomize sequence. Nucleic tools: Primer design.
CD-HITA series of programs for sequence comparisons. Creating non-redundant datasets for proteins. Clustering analysis of various types of DNAs and RNAs. Clustering 16S rRNA tags into OTUs (454, Iontorrent and Illumina reads). Generate protein families. Merge assembled contigs.
ConSeq ServerServer for the identification of functionally and structurally important residues in protein sequences.
CountcodonGenerates a codon usage table for the input sequence.
CpgreportIdentify and report CpG islands in nucleotide sequences.
EMBOSS SeqretSequence format conversion. Reformatting sequences, producing the reverse complement of a sequence, extracting fragments of a sequence, sequence case conversion or any combination of the above functions.
FMAPSequence alignment with genome. Maps sequence to human, rat and mouse genomes.
GeneMarkGene Prediction in Bacteria, Archaea and Metagenomes.
GenscanPredicting the locations and exon-intron structures of genes in genomic sequences from a variety of organisms.
MEME SuiteMotif-based analysis of DNA, RNA and protein sequences.
NEBcutterExamines DNA sequence to find large, non-overlapping open reading frames (ORFs) and sites for all restriction enzymes that cut the sequence just once.
ORF FinderORF Finder (Open Reading Frame Finder).
PROMALS3DAlignments for multiple protein sequences or structures using information from sequence database searches, secondary structure prediction, available homologs with 3D structures.
PictogramTool to visualize sequence alignments and consensus sequences showing the relative frequencies of the bases at each position.
PlasMapperGenerates and annotates plasmid maps using only plasmid DNA sequence as input. Figures may be rendered in PNG, JPG, SVG or SVGZ format.
PromoSerWeb-based service for extraction of a large number of promoter sequences from mammalian genomes.
RNA/DNA secondary structure prediction and designPairFold predicts the minimum free energy secondary structure formed by two input DNA or RNA molecules.
Restriction Map GeneratorAnalyzes a DNA sequence to identify Restriction Enzyme Sites and generate a comprehensive map overview of their locations within the DNA sequence.
Restriction MapperMaps sites for restriction enzymes (restriction endonucleases) in DNA sequences.
SOAP Short Oligonucleotide AnalysisProgram for faster alignment of short oligonucleotides onto reference sequences for next generation sequencing data analysis.
Sequence Manipulation SuiteJavaScript programs for generating, formatting, and analyzing short DNA and protein sequences.
SuperlinkGenetic linkage analysis with input-output relationships similar to those in standard genetic linkage programs.
TFBINDSearching transcription factor binding sites (TATA boxes, GC boxes, CCAAT boxes, transcription start sites (TSS).
TRACTSA program to map oligopurine.oligopyrimidine and other binary DNA tracts.
Trait-o-maticOpen-source tool to find and classify phenotypic correlations for variations in whole genomes.
VIROMEClassification of predicted open-reading frames (ORFs) from viral metagenomes.
VistaPrograms and databases for comparative analysis of genomic sequences.
WEGOWeb Gene Ontology Annotation Plot.