Tools for Sequence Analysis

http://bioinformatics.igc.gulbenkian.pt/resources/tools/sequenceanalysis/#sequence_manipulation

Sequence Manipulation

tool	description
SMS	Sequence Manipulation Suite - Here you can find a collection of programs for generating, formatting, and analyzing DNA and protein sequences.
MERGER	Tool from the EMBOSS package joins two overlapping nucleic acid sequences into one merged sequence.
Reverse	Tool to convert a DNA sequence into its reverse, complement, or reverse-complement .

Restriction Analysis

tool	description
REBASE	Restriction Enzyme Database - search for restriction enzymes by name, species, recognition sequence, companies that sell restriction enzymes or by authors and citations associated with each enzyme.
NEBcutter	A nice site for generating retriction maps and identification of non-overlapping ORFs.
Mapper	Generate several types of graphics and text-based maps for restriction enzymes.
WebCut	An on-line tool for restriction analysis, silent mutation scanning, and SNP-RFLP analysis.

Primer Design

Rules to design primers

tool	description
Primer3	Primer3 is a widely used program for designing PCR primers.
Primaclade	Application that accepts a multiple species nucleotide alignment file as input and identifies a set of PCR primers that will bind across the alignment. The program iteratively runs the Primer3 application for each alignment sequence and collates the results.
ProbeFinder	Design intron-spanning assays for your target gene. You can select the organism of interest and enter the target-gene name, gene ID or nucleotide sequence.
RT-Primer Design	Real Time PCR primer design.
CODEHOP	The Consensus-degenerate hybrid oligonucleotide primers program designs PCR primers from protein multiple-sequence alignments and is intended for cases where the protein sequences are distant from each other and degenerate primers are needed Help.
MEME for primer design	Method for designing degenerate primers based on multiple local alignments employing the MEME algorithm supported with electronic PCR.

Finding Genes

tool	description
GENSCAN	Gene identification program which analyzes genomic DNA sequences from a variety of organisms including human, other vertebrates, invertebrates and plants.
GeneMark	Package of programs for gene prediction in Bacteria, Archaea and Metagenomes; Eukaryotes; Viruses, Phages and Plasmids and EST.
Softberry	Gene finding in Eukaryote, Bacteria and Virus.
GrailEXP	Software that predicts exons, genes, promoters, polyAs, CpG islands, EST similarities, and repetitive elements within DNA sequence.
Generation	Software that performs gene predictions on microbial and model organisms and produce a set of data which can be used by GrailEXP v3.0 to recognize genes in these organisms.
DragonGSF	Prediction of gene start location in mammalian genomes, by combining information about CpG islands, transcription start sites (TSSs), and signals downstream of the predicted TSSs.
GeneWise	Software thar compares a protein sequence to a genomic DNA sequence, allowing for introns and frameshifting errors.
Link	A list of gene prediction programs for both eukaryotic and prokaryotic organisms.

Finding Promoters and Regulatory Elements

tool	description
TFSEARCH	Searching DNA for eukaryotic transcription Factor Binding Sites and DNA-binding profiles (searches TransFAC).
ConSite	Tool for finding cis-regulatory elements in genomic sequences. Predictions are based on the integration of binding site prediction generated with high-quality transcription factor models and cross-species comparison filtering (phylogenetic footprinting).
TESS	Web tool for predicting transcription factor binding sites in DNA sequences. It can identify binding sites using site or consensus strings and positional weight matrices from the TRANSFAC, JASPAR, IMD, CBIL-GibbsMat database. You can use TESS to search a few of your own sequences or for user-defined CRMs genome-wide near genes throughout genomes of interest.
Softberry	Gene finding in Eukaryote, Bacteria and Virus. Go to Test on Line on the left side, and seach onsearch Motifs menu.
NNPP	Neural Network Promoter Prediction - Promoter Prediction by Neural Network for prokaryotes or eukaryotes.
PromoterScan	Predicts Promoter regions based on scoring homologies with putative eukaryotic Pol II promoter sequences.
Promoter	Predicts transcription start sites of vertebrate PolII promoters in DNA sequences.

Identify Splice Junctions

tool	description
NNSPLICE	Splice Site Prediction by Neural Network for drosophila and human/other Help.
NetGene2	The NetGene2 server is a service producing neural network predictions of splice sites in human, C. elegans and A. thaliana DNA Help.
MaxEntScan	MaxEntScan was used to score the splice site signals of each exon-intron junction. MaxEntScan is based on the approach for modeling the sequences of short sequence motifs such as those involved in RNA splicing which simultaneously accounts for non-adjacent as well as adjacent dependencies between positions.
SROOGLE	The Splicing RegulatiOn Online Graphical Engine combines: 1)Availability of data - accessibility to large sets of published data; 2) Integration of data - integrative overview of the signals characterizing exons of interest; 3) Intuitive statistical measures -many algorithms provide output which are not directly interpretable (e.g. delta-G scores, PSSM log odd scores), etc.. 4) User friendliness - intuitive, interactive, graphical user interface and on dynamic java-script programming, enabling users to interactively modify their input. Help.
HSF	The Human Splicing Finder is an online bioinformatics tool to predict the effects of mutations on splicing signals or to identify splicing motifs in any human sequence. Help.
SplicePort	SplicePort is a splice-site analysis tool that makes splice-site predictions for submitted sequences, and allows browsing of predictive signals and motif exploration. This collection of signals is capable of achieving high classification accuracy on human splice sites. Help.
ASSP	Prediction of putative alternative exon isoform, cryptic, and constitutive splice sites of internal (coding) exons Help.

Sequence repeat finders

tool	description
RepeatMasker	Program that screens DNA sequences for low complexity DNA sequences and interspersed repeats. The masked out sequence can be used for example BLAST searches. Repeats are stored in the datbase Repbase update.

Sequence Motif Finders

tool	description
Sequence Motif Finder	Scan Nucleotide or Protein Sequences for Matching Patterns.
ELPH	Estimated Locations of Pattern Hits - Find motifs in a set of DNA or protein sequencesTutorial.

Translation Tools

tool	description
Transeq	Tool from the EMBOSS package, translates nucleic acid sequences to the corresponding peptide sequence. It has option for which Genetic Code Table to use.
Translate	This tool allows the translation of a nucleotide (DNA/RNA) sequence to a protein sequence using the standard genetic code.
ORF Finder	Open Reading Frame Finder is a graphical analysis tool which finds all open reading frames of a selectable minimum size in a user’s sequence or in a sequence already in the database using the standard or alternative genetic codes.

Post-Translational Modifications

tool	description
PTM Tutorial	Post-translationam modification tutorial.
PTM prediction tools	A survey of publicly available PTM web resources, databases and classification/prediction servers.
GlycoMod	Tool that can predict the possible oligosaccharide structures that occur on proteins from their experimentally determined masses. The program can be used for free or derivatized oligosaccharides and for glycopeptides.
Myristoylator	This tool predicts N-terminal myristoylation of proteins by neural networks.Only N-terminal glycines are myristoylated (leading methionines are cleaved prior to myristoylation).
GPS	Group-based Phosphorylation Scoring method is a tool for in silico prediction of phosphorylation sites with their specific kinases.
NetPhos	Tool that produces neural network predictions for serine, threonine and tyrosine phosphorylation sites in eukaryotic proteins.
SUMOsp	Tool for in silico sumoylation sites prediction. SUMOylation, a reversible post-translational modification of proteins by the small ubiquitin-related modifiers (SUMO), is crucial in a variety of biological processes.

Align Two Sequences

tool	description
bl2seq	This tool produces the alignment of two given sequences using the NCBI BLAST engine for local alignment. The output shows the similar region.
Needle	EMBOSS Pairwise Alignment Algorithms tool used to compare 2 sequences when you want an alignment that covers the whole length of both sequences.
Water	EMBOSS Pairwise Alignment Algorithms tool used when you are trying to find the best region of similarity between two sequences.

Multiple Sequence Alignment

tool	description
Multalin	Multiple sequence alignment for DNA or proteins with hierarchical clustering.
ClustalW	Multiple sequence alignment program for DNA or proteins sequences. It calculates the best match for the selected sequences, and lines them up so that the identities, similarities and differences can be seen. Evolutionary relationships can be seen via viewing Cladograms or Phylograms.
Tcoffee	Computes a multiple sequence alignment and the associated phylogenetic tree for a set of sequences (Proteins or DNA). T-Coffee allows the combination of a collection of multiple/pairwise, global or local alignments into a single model. It also allows to estimate the level of consistency of each position within the new alignment with the rest of the alignments.

BLAST

tool	description
BLAST	The Basic Local Alignment Search Tool (NCBI) finds regions of local similarity between sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches Tutorial.
Blast@EBI	Here you can find a list of all the Blast´s available at the EBI including the Ensembl Multi BlastView to the annotated genomes.