genbank mirror ID search

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history of uhmin tools (Japanese only)

This page is going to be closed at the end of February 2017 due to replacement of the host computer system.
So, I am making a shelter on a rental server. Users can keep using most of the tools on the shelter .
Any questions and/or comments are welcome.

Coloring of alignment 2 NEW! (12' Sep. 24)

You can add color to your sequence. The second version of "Coloring of alignment".

SqdifPlot ^{UP DATE! (13' Apr.5)}

This software calculate rates synonimous and non-synonimous changes, using Miyata-Yasunaga or Nei-Gojobori method.

Color-Bar Plot

Create Color-Bar from your tabular data.

Count sequence population

This program counts the identical sequences and shows unique sequences descending order. This program also estimates Shannon-Weaver diversity index (H).

GO homology

This program presumes Gene Ontologies of submited sequences.

Z-matrix Converter

This program converts Z-matrix data from gamess output format to Winmostar format.

extractCD

CDsearch performs RPS-BLAST search against NCBI CDD database. Subsequences of the homologous region of the most conserved domain for each of the input sequence will be extracted.

CCResid

CCResid compares control sequences and test sequences and highlights those residues in test sequences that are conserved in control sequences.

CGI checker

You can see with this web service what kind of informations are sent when you submit.

consensus

Search for consensus sequence from aligned sequences.

Histogram

Display histogram from input numeric data.

On Demand Mapping

Automatic mapping system using {sim4 or BLAT} and megablast.

Annotation helper

Perform BLAST search with ncbi nr database

Output format is optimised for deciding annotations.

genbank mirr ID search

This service will show you nucleotide or amino acid sequence from our mirror database of GenBank.

Genome Mapping Viewer on Web

Mapping database of Human and Mouse genome

Blastmatrix. A homology matrix tool powered by BLAST

High speed homology matrix drowing.

Available untill some mega-base-pair sequence.

Multi blastmatrix. A new version of blastmatrix.

This new blastmatrix can make a homology matrix of multifasta sequence.

You can see multiple alignment more easily

ORF finder

Extract ORF from multifasta sequence.

It can translate nucleotide sequence to amino acid sequence.

reverse complement

Return reverse and/or complement sequence of input multifasta sequence.

ooTFD mirr

Because original ooTFD requires JAVA applet, and it does not suite for mass processing, I created a CGI for my convenience.

get upstream region of transcription start sites of RIKEN FANTOM cDNA clones.

for the genomic sequence UCSC mm5 is employed.

Nucleic and/or Amino Acid contents

Calculate GC-contents and other from multifasta nucleotide sequence.

GO chase

Searches Gene Ontology annotations.

PRESERVE

Calculate emerge frequency of N-letter sequence

Need Assemble?

Assemble patterns which were listed by PRESERVE.

Multiple alignment ^{UP DATE! (13' Apr.5)}

Alignment with clustalw or mafft.
You can now align nucleic sequences considering amino acid frame.
Select "tranalign" mode. This mode will translate the input sequence and align using mafft auto mode. Finally, the alignment will be refrected to the nucleotide sequence by tranaglign program.

Coloring of alignment

Useful when you want to color your alignments.

Convert alignformat to multifasta format

Useful when you wanto to convert alignment format data to multifasta format.

DoCoNo

Search key sequence(s) from query multifasta sequence.

Text analysis

List frequently apperaing word(s). English text only.

Gene Web III

We are prouded of our gene analysis tools GeneWeb III