In silico analysis tools (bioinformatics) : nucleic acids techniques

IN SILICO ANALYSIS TECHNIQUES (BIOINFORMATICS) - NUCLEIC ACIDS TOOLS
(see also multicellular Eukarya sequencing projects

and immunoinformatics

)

"There have been some discussions lately about the appropriate balance between access to genomic data and global security^ref. In our view, the awareness that we have technology to develop vaccines that will render any biological weapon inoffensive is a strong deterrent for bioterrorism. Conversely, restrictions on the sharing of genomic information would represent a recognition of weakness and only serve to encourage the development of biological weapons."

Rino Rappuoli^ref

databases of polinucleotide sequences

find homologies

create restriction maps

genome aligners

find CpG motifs in DNA

design PCR primers

DNA => RNA transcription

find regulatory regions in genomic DNA

find transcription factors (TFs) binding site in a sequence

RNA secondary structure prediction

miRNA

DNA => protein translation

ORF analysis
prediction of exons or coding regions
predictions of exons and gene structure

visualization tools

miscellanea

Guide to Molecular Sequence Analysis
Multipurpose Automated Genome Project Investigation Environment (MAGPIE)
available via wireless application protocol (WAP) :

BioWAP at University of Tampere, Finland
Wireless Genome Information Database (WiGID) by Björn Ursing, CGB, Karolinska Institutet, Sweden

databases of polinucleotide sequences

GenBank (to submit your new nucleotide sequence to GenBank use Sequin or Banklt)
EMBL (to submit your new nucleotide sequence to EMBL use Webin)
DNA Data Bank of Japan (DDBJ) (to submit your new nucleotide sequence uto DDBJ use Sakura)
UniGene : automatically partition of GenBank into non-redundant set of gene-oriented clusters
ESTs and THCs

find homologies

Sequence Alignment : principles, algorithms and parameters
Weight matrices for sequence similarity scoring : BLOSUM and PAM (percent accepted mutation, a.k.a. accepted point mutation)
AUTHORIN-Genbank sequence submission program via ftp from NCBI
MACAW-Multiple Alignment Construction & Analysis Workbench program for Windows and Macintosh via ftp from NCBI
Basic Local Alignment Search Tool (BLAST)

comparing a nucleotide query sequence against a nucleotide sequence database (blastn)
comparing the 6-frame translations of a nucleotide query sequence against a protein sequence database (blastx)
comparing the 6-frame translations of a nucleotide query sequence against the six-frame translations of a nucleotide sequence database (tblastx)

ClustalW : align two or more DNA sequences (use Netscape Navigator !)
SRS v.6.0 at EBI

designs plasmids, cosmids, etc.

Gene Construction Kit by Textco
SimVector by PREMIER Biosoft International
BVTech Plasmid 1.0
Vector NTI Suite
bioedit is a freeware tool
DNAman
NetPrimer

create restriction maps for a given DNA sequence :

Restriction Enzyme Database (REBASE) : restriction enzymes, methylases, the microorganisms from which they have been isolated, recognition sequences, cleavage sites, methylation specificity, the commercial availability of the enzymes, and references.

genome aligners :

AVID
BLASTZ
BLAT
Exonerate
GLASS
LAGAN/MLAGAN
MegaBLAST
MUMmer
PatternHunter
Cross-Species Alignments by Jim Kent
whole genome alignments in genome browser :

ECR browser
Ensembl
UCSC
PipMaker and MultiPipMaker (pdf output only)
VISTA Browser (VGB2)
WormBase

find CpG motifs in DNA :

CpG Island Searcher^ref

design PCR primers :

MFEprimer for evaluating the specificity of PCR primers based on multiple factors, including sequence similarity, stability at the 3' end of the primer, melting temperature, GC content, and number of binding sites between the primer and DNA templates (free download) ^ref
Primer3Plus
BatchPrimer3^ref

DNA => RNA transcription :

find regulatory regions in genomic DNA

Nature Immunology tutorial^{ref1,
ref2,
ref3,ref4,
ref5,
ref6,
ref7,
ref8,
ref9,
ref10}
finding regulatory regions by phylogenetic footprinting

companies offering bioinformatics software for gene expression and pathway analysis : Acumenta, Affymetrix, Agilent Technologies, Applied Biosystems, Applied Maths, Applied Precision, Ariadne Genomics Inc., Array Genetics, Axon Instruments, Bioalma, BioBase, BioConductor, BioDiscovery, Bioinformatics Solutions Inc, Bio-Rad Laboratories, BioSoftSolutions, BIOSoftware Systems Inc., Clondiag Chip Technologies, Compugen, Decodon, GeneData, GeneGo, Geneva Bioinformatics (GeneBio) S.A., Genotypic Technology, Imaging Research, Improved Outcomes Software, InforSense, Ingenuity Systems, Insightful, Insilicos, Invitrogen, Iobion, Jubilant Biosys, LION bioscience AG, MediaCybernetics, Metalife AG, MiraiBio, MolMine, NonLinear Dynamics, Paracel, Partek, Proteome Systems, Rosetta Biosoftware, Scanalytics, SilicoCyte, Silicon Genetics, Stratagene, TIGR, Universal Imaging, Visualize Inc., VizXlabs
find transcription factors (TFs) binding site in a sequence

TFSEARCH : searching Transcription Factor Binding Sites
TRANSFAC 5.0 : a database for proteins involved in transcriptional regulation
MatInspector
Transcription Regulatory Region Database (TRRD)

GeneMarkS : improving the accuracy of prediction of gene starts is one of a few remaining open problems in computer prediction of prokaryotic genes. Its difficulty is caused by the absence of relatively strong sequence patterns identifying true translation initiation sites. The accuracy of gene start prediction can be improved by combining models of protein-coding and non-coding regions and models of regulatory sites near gene start within an iterative Hidden Markov model based algorithm. The new gene prediction method, called GeneMarkS, utilizes a non-supervised training procedure and can be used for a newly sequenced prokaryotic genome with no prior knowledge of any protein or rRNA genes. The GeneMarkS implementation uses an improved version of the gene finding program GeneMark.hmm, heuristic Markov models of coding and non-coding regions and the Gibbs sampling multiple alignment program^ref.

viral genomes online (VIOLIN) : annotations of viral genomes obtained by the GeneMark gene prediction programs

RNA secondary structure prediction :

miRNA :

miRNAMap at National Chiao Tung University in Taiwan

DNA => protein translation

Translate - Translates a nucleotide sequence to a protein sequence
Protein machine - Nucleotide to protein translation at EBI
JustBio translator - Nucleotide to protein translation at MBS
Backtranslation tool V2.0 - Translates a protein sequence back to a nucleotide sequence
Wise 2 - Compares a protein sequence to a genomic DNA sequence, allowing for introns and frameshifting errors
Frameshift error detection (FSED)
LabOnWeb - Elongation, expression profiles and sequence analysis of ESTs using Compugen LEADS clusters
List of gene identification software sites

ORF analysis

ORF Finder (NCBI)
ORF analysis (WebGene)

prediction of exons or coding regions

Dialign 2.2.1
prediction of intronic splicing enhancers (ISEs)

RESCUE-ISE

prediction of exonic splicing enhancers (ISEs)

RESCUE-ESE predicts which sequences have ESE activity by statistical analysis of exon-intron and splice site composition^ref

predictions of exons and gene structure

GeneXPress is a visualization and analysis tool for gene expression data, integrating clustering, gene annotation, and sequence information. GeneXPress allows you to load clustering results and automatically analyze them for significance of functional groups through correlation with functional annotations (e.g. Gene Ontology) and for enrichment of motif binding sites (e.g. TRANSFAC motifs).
database of Genotype and Phenotype (dbGaP) at NCBI
visualization tools

miscellanea

The travelling salesman problem
EST-PAGE (P (Processing of chromatograms including base calling); A (Analysis of the sequence data with vector masking, low complexity filtering, and E.coli contamination screening); G (GenBank dbEST submission), E (Exploration of EST data by clustering and annotation))
PRODORIC

Search
for