BLAST nucleotide (BLASTN) searches nucleotide subjects using a nucleotide query.
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Multiple Sequence Alignment is the arrangement of several protein or nucleic acid sequences with postulated gaps so that similar residues (in one-letter code) are juxtaposed.
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ClustalW2 is a general purpose multiple sequence alignment program for DNA or proteins. The online version is hosted by EMBL. It produces biologically meaningful multiple sequence alignments of divergent sequences. It calculates the best match for the selected sequences, and lines them up so that the identities, similarities and differences can be seen.
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Compare two sequences aligns two sequences using the indicated algorithm, and calculates the statistical significance using shuffled sequences.
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LALIGN/PLALIGN find internal duplications by calculating non-intersecting local alignments of protein or DNA sequences. LALIGN shows the alignments and similarity scores, while PLALIGN presents a "dot-plot" like graph.
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Dotlet is a program for comparing sequences by the diagonal plot method. It is designed to be platform-independent and to run in a Web browser, thus enabling the majority of researchers to use it.
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PRALINE is a multiple sequence alignment program with many options to optimise the information for each of the input sequences; e.g. homology-extended alignment, predicted secondary structure and/or transmembrane structure information and iteration capabilities.
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YASS is a genomic similarity search tool, for nucleic (DNA/RNA) sequences in fasta or plain text format (it produces local pairwise alignments).
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SCAN2 is a we app for aligning two multimegabyte-size genome sequences
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PipeAlign2 is a protein family analysis tool integrating a multi-step process ranging from the search for sequence homologues in protein and 3D structure databases to the structural / functional annotation of the family. The complete, automatic pipeline takes a single sequence or a set of sequences as input and constructs a high-quality, validated multiple sequence alignment (MSA) in which sequences are clustered into potential functional subgroups.
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zPicture is a dynamic alignment and visualization tool that is based on blastz alignment program utilized by PipMaker. zPicture alignments can be automatically submitted to rVista 2.0 to identify conserved transcription factor binding sites.
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Java Dot Plot Alignments (JDotter) is a platform-independent Java interactive interface for the Linux version of Dotter, a widely used program for generating dotplots of large DNA or protein sequences. JDotter runs as a client-server application and can send new sequences to the Dotter program for alignment as well as rapidly access a repository of preprocessed dotplots. JDotter also interfaces with a sequence database or file system to display supplementary feature data. Thus, JDotter greatly s
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ESPript, 'Easy Sequencing in PostScript', is a program which renders sequence similarities and secondary structure information from aligned sequences for analysis and publication purpose.
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VISualization Tools for Alignments: VISTA is a comprehensive suite of programs and databases for comparative analysis of genomic sequences.
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While standard alignment methods rely on comparing single residues and imposing gap penalties, DIALIGN constructs pairwise and multiple alignments by comparing entire segments of the sequences. No gap penalty is used. This approach can be used for both global and local alignment, but it is particularly successful in situations where sequences share only local homologies.
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H-BloX is a web-based JavaScript application that allows one to calculate and visualize the Shannon information or the relative entropy (Kullback-Leibler distance) of sequence alignment blocks. Various residue alphabets may be defined and useful modifications of the alignment block and the alphabet can be applied before calculation.
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PipMaker computes alignments of similar regions in two DNA sequences. The resulting alignments are summarized with a ``percent identity plot'', or ``pip'' for short. MultiPipMaker allows the user to see relationships among more than two sequences. All pairwise alignments with the first sequence are computed and then returned as interleaved pips. Moreover, MultiPipMaker can be requested to compute a true multiple alignment of the input sequences and return a nucleotide-level view of the results.
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Compare gene order between two small bacterial genomes
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GeConT (Gene Context Tool) is a web interface designed to visualize genome context of a gene or a group of genes and their orthologs in all the completely sequenced genomes. The graphical information of GeConT can be used to analyze genome annotation, functional ortholog identification or to verify the genomic context congruence of any set of genes that share a common property.
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CClustal Omega is the latest addition to the Clustal family of general purpose multiple sequence alignment programs for DNA, RNA or proteins. The online version is hosted by EMBL. It offers a significant increase in scalability over previous versions, allowing hundreds of thousands of sequences to be aligned in only a few hours. It will also make use of multiple processors, where present. In addition, the quality of alignments is superior to previous versions, as measured by a range of popular b
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