DNA/RNA ANALYSIS TOOLS
ALIGN
(Optimal Global Alignment of Two Sequences with No Short-cuts)
BEAUTY (BLAST Enhanced Alignment Utility)
LALIGN
(Calculates the N-Best Local Alignments Between Two Sequences)
MSA (Multiple Sequence Alignment)
Multiple Sequence Alignments (CLUSTAL-W, MAP, and PIMA alignments)
BOXSHADE
(Printing and Shading of Multiple-Sequence Alignments)
FASTA (United Kingdom)
(Compare nucleic acid sequence with those in a database)
FASTA (Stanford)
FASTA (EERIE)
FASTA (CRIHAN)
FASTPAT
(FASTA-based Pattern Database Search)
LFASTA
(Local Similarity Searches Between Two Sequences Showing Local Alignments)
Seqanalref
(Sequence analysis bibliographic reference data bank)
Seqanalref
at Harvard)(Sequence analysis bibliographic reference data bank)
Codon Usage
(Analysis of Different ORFs in a Gene Sequence)
Darwin
(Data Analysis and Retrieval With Indexed Nucleotide/Peptide Sequences)
Dot plot
(Comparison of a DNA Sequence with Itself)
Gene Finder
(Predict gene structure, exons & splicing sites in DNA & exon-exon junction in cDNA )
GenLang
(Find Genes and Other Higher-Order Features in Nucleotide Sequences)
PatScan (Pattern Matches in DNA or Protein Sequences)
Plant EST Analysis
(Similarity Analysis of Different Plant cDNA/EST Sequences)
PHILIP-Bootstrapping Analysis
(Divergence Between Protein or Nucleotide Sequences)
BIOACCELERATOR(Conduct homology searches)
Poland
(Calculate the Thermal Denaturation Profile of Double Stranded RNA or DNA)
Extinction Coefficient Calculation
ProfileScan
(Search a Sequence Against a Library of Profiles)
RSVP
(Rapid Sequence Visualization in Postscript for Analysis of DNA
Sequences)
SSEARCH
(Universal Sequence Comparison Using the Smith-Waterman Algorithm)
Sequence
Annotation (Annotations on NCBI
Sequences)
Sequence
Translation
(Translate Gene Sequences)
Translate
(Translate a Nucleotide Sequence to a Protein)
RNA Secondary
Structures (Information on Group I Introns and rRNA)
Finding Splice Sites
Primer
(Select PCR Primers in a Gene Sequence)
Tm (Oligonucleotide Melting Point Determination)
WebLogo
(Sequence Logo Generation)
STS Pipeline
(Analysis & STS Primer Picking of Short DNA Sequences with
Duplicate Checking, Sequence Repeat Finding, Restriction Analysis,
Vector Identification and BLAST Searching)