NOVELTIES
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. Registration not required.
Click here for more informationsPublished on 2010-07-11 00:00:00
The Wise2 form compares a protein sequence to a genomic DNA sequence, allowing for introns and frameshifting errors. Registration not required.
Click here for more informationsPublished on 2010-07-11 00:00:00
SDS (siRNA Design Software) is a software tool that helps to design siRNAs for silencing gene expression. The tool takes an mRNA sequence and makes use of existing design tools to output a set of candidates. These candidates are then filtered based on the secondary structure. With the following features: It provides a unified platform for using existing software. It compares the output of existing software. It enhances the existing software by filtering ineffective siRNAs based on secondary structure. Registration not required.
Click here for more informationsPublished on 2010-07-10 00:00:00
ESPript, 'Easy Sequencing in PostScript', is a program which renders sequence similarities and secondary structure information from aligned sequences for analysis and publication purpose. Registration not required.
Click here for more informationsPublished on 2010-06-28 00:00:00
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. Registration not required.
Click here for more informationsPublished on 2010-06-28 00:00:00
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. Registration not required.
Click here for more informationsPublished on 2010-06-28 00:00:00
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 simplifies access to dotplot data in laboratories that deal with large numbers of genomes and have a multi-platform organization. Registration not required.
Click here for more informationsPublished on 2010-06-28 00:00:00
YASS is a genomic similarity search tool, for nucleic (DNA/RNA) sequences in fasta or plain text format (it produces local pairwise alignments). Registration not required.
Click here for more informationsPublished on 2010-06-28 00:00:00
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. Registration not required.
Click here for more informationsPublished on 2010-06-28 00:00:00
Compare gene order between two small bacterial genomes Registration not required.
Click here for more informationsPublished on 2010-06-28 00:00:00
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. Registration not required.
Click here for more informationsPublished on 2010-06-28 00:00:00
COBALT computes a multiple protein sequence alignment using conserved domain and local sequence similarity information. Registration not required.
Click here for more informationsPublished on 2010-06-28 00:00:00
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Home Recent Results Saved Strategies Needleman-Wunsch Global Align Nucleotide Sequences
Category: Protein sequences alignment
The Needleman-Wunsch global alignment (now hosted by BLAST/NLM) performs a global alignment on two sequences. It is commonly used in bioinformatics to align protein or nucleotide sequences. Registration not required.
Click here for more informationsPublished on 2010-06-28 00:00:00
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. Registration not required.
Click here for more informationsPublished on 2010-06-28 00:00:00
FOLDALIGN is an algorithm for local or global simultaneous folding and aligning two or more RNA sequences and is based on the Sankoffs algorithm (SIAM J. Appl. Math., 45:810-825, 1985). Foldalign can make pairwise local or global alignments and structure predictions. FoldalignM makes a multiple global alignment and structure prediction. Registration not required.
Click here for more informationsPublished on 2010-06-28 00:00:00
Overlapping Primers creates multiple overlapping PCR products in one sequence. Registration not required.
Click here for more informationsPublished on 2010-06-28 00:00:00
designs primers around exons in genomic sequence. All you need is a GenBank file containing your gene. Registration not required.
Click here for more informationsPublished on 2010-06-28 00:00:00
designs primers around every SNP in a GenBank file. Registration not required.
Click here for more informationsPublished on 2010-06-28 00:00:00
designs primers around open reading frames. Simply upload a GenBank file containing your genes. Registration not required.
Click here for more informationsPublished on 2010-06-28 00:00:00
multi-objective multiplex PCR assay design - designed for large-scale multiplex PCR assay design in an automated high-throughput environment, where high coverage is required. Registration not required.
Click here for more informationsPublished on 2010-06-28 00:00:00
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