Comparing sequences against a database
BLAST
BlastHome @NCBI
@BCM
@JGC
@French
FASTA @UK
@ORNL U.S.
@French
BLITZ (Sequence similarity search of the SwissProt Database)
BEAUTY Nucleic Acid
@BCM
Protein @BCM
Contig Assembly
CAP Contig Assembly Program for Sequence Fragment Alignment and Assembly
GCG Software Package
Staden Software Package
Predicting Protein-coding Region
cDNA
DNA to protein translation <
Mirror site @Taiwan>
Frameshift Error Detection
Genewise (compares a protein sequence to a genomic DNA sequence)
MaxORF (Java enable browser required) @Joyce BioNetwork
MBS translator @MBS DNA Seq to Peptide Seq
ORF finder a graphical analysis tool which finds all open reading frames
WebGene
Tools for prediction and analysis of protein-coding gene structure (Italy)
Translation Machine @EBI DNA Seq to Peptide Seq
Genomic DNA
GRAIL
DNA Analysis
Restriction enzyme maps
EnzFinder restriction enzyme search engine @MBS
REBASE (restriction enzyme database)
Webcutter an
on-line tool for restriction mapping nucleotide sequences
Promoters and other DNA control sites
HCPolyA
(Hamming Clustering Method) Poly-A Site Prediction @WebGene
HCtata Hamming Clustering Method for TATA signal prediction in Eukaryotic Genes
Human Core-Promoter Finder
MatInspector/TRANSFAC Professional Version
NNPP
(Promoter Prediction by Neural Network)
POLYAH
Recognition of 3'-end Cleavage & Poly-A Signals
PROMOTER SCAN II
TESS
TFSEARCH
(Transcription Factor Search)
Exon, Intron prediction
CpG @WebGene CpG islands prediction
FEXH
Genie
(A gene finder based on generalized hidden Markov Model)
HEXON
HSPL
MZEF (Human Internal Coding Exon Finder)
NNSSP
(Splice Site Prediction by Neural Network)
Repeat
@WebGene Repeated elements mapping
RepeatMasker2 it screens DNA sequences in fasta format against a library of repetitive elements and returns a masked query sequence ready for
database searches as well as a table annotating the masked regions
SpliceView Splicing signals prediction @WebGene
Primer Analysis
Primer3 (old version) Primer3 New version Primer Picker
Primer Selection (xprimer base)
Tm Determination @U. Minnesota
RNA secondary structure prediction
MFOLD for PC (filename: pcfldsrc.uue)
for Unix
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