Sequence Analysis

Sequence analysis encompasses the use of various bioinformatic methods to determine the biological function and/or structure of genes and the proteins they code for.

Tools such as Transeq can help determine the protein coding regions of a DNA sequence. ClustalW2 is use to align DNA or protein sequences in order to elucidate their relatedness as well as their evolutionary origin.

The following are links to the various structural analysis tools we have available at the EBI.

Tool	Description
Align	Pairwise global and local alignment tool (EMBOSS).
CENSOR	Screen query sequences against a reference collection of repeats.
ClustalW2	Multiple sequence alignments.
CpG Plot/CpGreport	CpG Island finder and plotting tool (EMBOSS).
Dna Block Aligner Form	Compares two DNA sequences assuming colinear blocks, ideal for promoters.
GeneWise	Compares a protein sequence or a protein profile HMM to a DNA sequence.
Kalign	A fast and accurate multiple sequence alignment algorithm.
MAFFT	MAFFT (Multiple Alignment using Fast Fourier Transform) is a high speed multiple sequence alignment program.
MUSCLE	MUltiple Sequence Comparison by Log-Expectation, claimed to achieve both better average accuracy and better speed than ClustalW2 or T-Coffee, depending on the chosen options.
Pepstats/Pepwindow/Pepinfo	EMBOSS programs for basic protein sequence analysis (EMBOSS).
PromoterWise	Compares two DNA sequences allowing for inversions and translocations, ideal for promoters.
SAPS	Statistics on protein sequences.
T-Coffee	A multiple sequence alignment program that Allows you to combine results obtained with several alignment methods.
Transeq	DNA sequence translation tool (EMBOSS).
webPRANK	webPRANK is a phylogeny-aware multiple sequence alignment program which makes use of evolutionary information to help place insertions and deletions

EMBOSS

• Align Pairwise global and local alignment tool
• CpG Plot/CpGreport CpG Island finder and plotting tool
• Transeq DNA sequence translation tool
• Pepstats/Pepwindow/Pepinfo

EMBL Tools