A sequence alignment is a schematic arrangement of one sequence of DNA, RNA and protein sequences on top of another where the residues in one position are entitled to have a common evolutionary origin. This method is used to identify regions of similarity that may be a consequence of functional, structural, or evolutionary relationships between two or more sequences.

Tool Name



It finds multiple matching sub-segments in two sequences. It provides or assigns one with % identity for different sub-segments of the sequence.


It presents the output file in graphical and numerical form of % identity between two proteins, or RNA or DNA molecules.


It provides base calling, chromatogram display and high quality sequence region evaluation and presentation. It can align up to five sequences simultaneously.

GeneOrder 2.0

It is an ideal tool for the alignment of small GenBank genome sequences (upto 0.25Mb). It has a new version as GeneOrder 3.0. There are two display formats: graphical and tabular.


It is designed to analyze two to five genomes simultaneously, it also generates a table of related genes i.e. orthologs and putative orthologs. It has a limit of 0.35 Mb. It has an updated version CoreGenes 2.0


This is the web version of ACT (Artemis Comparison Tool) a DNA sequence comparison viewer based on Artemis (Reference: T.J. Carver et al. Bioinformatics 21: 3422 - 3423).


It is known as Bacterial Annotation Tool. It is far-fetched tool which supports automated and in-depth annotation of bacterial genomic sequences. BASys uses >30 programs to determine 60 annotation subfields for each gene, including gene/protein name, GO function, COG function, possible paralogues and orthologues, molecular weight, isoelectric point, operon structure, subcellular localization, signal peptides, transmembrane regions, secondary structure, 3D structure, reactions and pathways. (Reference: G.H. Van Domselaar et al. 2005. Nucl. Acids Res. 33(Web Server issue):W455-W459).


Works very well and quickly with phage-sized genomes. It also offers a choice of Glimmer, ZCurve or GeneMark predictions coupled with GenBank or Fasta-formatted output.


It stands for MIcrobial genome Checker. It enables rapid verification of sets of annotated genes and frameshifts in previously published bacterial genomes, or genomes for which the user has a *.gbk file.


It is an efficient program. Used for finding full-length LTR retrotranspsons in genome sequences. The input file size is limited to 50MB (Reference: Z. Xu & H. Wang. 2007. Nucl. Acids Res.35(Web Server issue): W265-W268).


To access this tool one requires to have user login. For pairwise alignment it requires a variety of output formats.


It is basically used for DNA sequence alignment. It is a local sequence alignment tool. It provides small graphic representation also which is very useful for only proteins or short DNA sequences.


It is an inbuilt part of the EMBOSS group of programs. This tool uses 10 and 0.5 as the default values for Gap opening and Gap extension penalty, respectively.


It is also a part of EMBOSS. It finds the best local alignments between two the sequences


It finds the best global alignment between the two sequences.


This tool folds and align RNA structures. based on a lightweight energy model and sequence similarity. The current version makes pairwise foldalignments. (Reference: J. H. Havgaard et al. 2005. Bioinformatics 21: 1815 - 1824).


It is a DNA or genome alignment and visualization tool based on blastz alignment program. Alignments can be automatically submitted to rVista 2.0 to identify evolutionary conserved transcription factor binding sites.


It is a Multiple Sequence Alignment search tool. This provides one with a number of options for data presentation, homology matrices [BLOSUM (Henikoff), PAM (Dayhoff) or GONNET, and presentation of phylogenetic trees (Neighbor-Joining, Phylip or Distance). (EBI, United Kingdom


DbCluster aligns sequences from a BlastP database search with one query sequence. The alignment algorithm is based on ClustalW modified to incorporate local alignment data in the form of anchor points between pairs of sequences. (Thompson et al. 2000. Nucleic Acid Research 28: 2919-2926; IGBMC, France)


A novel tool for generating multiple alignments of protein sequences. Using a combination of probabilistic modeling and consistency-based alignment techniques, PROBCONS has achieved the highest accuracies of all alignment methods to date.


A multiple sequence alignment program with many options to optimize the information for each of the input sequences; e.g. global or local preprocessing, predicted secondary structure information and iteration capabilities. (Reference: V.A. Simossis et al. (2005) Nucleic Acids Res. 33: 816-824). A similar type of output can be obtained using SPEM (Laboratory of Biophysics & Bioinformatics, University of Buffalo, U.S.A.).


DIALIGN is a novel program for multiple alignment developed by Burkhard Morgenstern et al. While standard alignment methods rely on comparing single residues and imposing gap penalties, DIALIGN constructs pairwise and multiple alignments by comparing whole segments of the sequences. (Univ. Bielfeld, Germany)


T-COFFEE is more accurate than ClustalW for sequences with less than 30% identity. The Output in aln, GCG/MSF and phylip formats.


Stands for Multiple Alignment of RNAs. A multiple sequence alignment of RNA’s taking into consideration both the primary sequence and the secondary structure. (Reference: S. Siebert & R. Backofen. 2005. Bioinformatics 21: 3352 - 3359).


It provides one with a colour-coded graphical alignment of genome length DNAs in Java. In the top panel regions of high sequence identity are presented in red.


A Java Dot Plot Viewer - a dot matrix plotter for Java. Produces similar diagrams to the above mentioned programs, but with better control on output. (Viral Bioinformatics Resource , University of Victoria, Canada)


Perform DNA local alignments with results in dotplot and tabular form (Reference: L.Noe & G. Kucherov. 2005. Nucl. Acids Res. 33: W540-W543).


(Reference: T.Junier & M. Pagni. 2000. Bioinformatics 16:178-179)


Provides nice dotplot graphs and dynamic visualization on multiple sequence alignment. zPicture alignments can be automatically submitted to rVista to identify conserved transcription factor binding sites. (Comparative Genomics , Lawrence Livermore National Laboratory, U.S.A.)

CoreGenes 3

Tallies the total number of genes in common between the two genomes being compared; displays the percent value of genes in common with a specific genome; determines the unique genes contained in a pair of proteomes. (D. Seto & P. Mahadevan, Bioinformatics & Computational Biology, George Mason Univ., U.S.A)


Offers an integrated approach to protein family analysis through a cascade of five different sequence analysis programs. Reference: F. Plewniak et al. 2003. Nucleic Acids Research, 31: 3829-3832


Very convenient since it permits one to specifically search databases such as prokaryote, bacteriophage, fungal, & 16S rRNA using BLASTN, and specific bacterial genomes or SwissProt using BLASTX or BLASTN.. (European Molecular Biology network - Swiss node)


Employs a heuristic method for sequence alignment. In essence, ParAlign is about as sensitive as Smith-Waterman but runs at the speed of BLAST. It presents nice graphics.


VISualization Tools for Alignments - this URL allows one to align two genome-length sequences. (Ernest Orlando Lawrence Berkeley National Laboratory, U.S.A.)


This tool was developed by was developed by Michael V. Graves for DNA or protein BLAST sequence analysis against the NCBI databases. It allows one to submit a file that contains multiple sequences and then will organize the results by each individual sequence contained in the file.


Stands for position-Specific Iterative BLAST and creates a profile after the initial search. This is used for subsequent searches.


It is used for pairwise alignment. Presentation of result file is very nice but server can be very slow. (Reference: Jaroszewski et al. 2005. Nucl. Acids Res. 33: W284-W288)