All-IN-ONE SEQ-ANALYZER
http://www-personal.umich.edu/~ino/blast.html
User's Mannual






Index

Introduction
 
All-IN-ONE SEQ-ANALYZER is the Web site to allow you analyze your DNA/protein sequence easily and simply.

This site is just like an on-line version of stand-alone DNA analysis programs that you are using. You no longer need to repeat "Cut & Paste" of your sequences to such programs nor the equivalent Web sites! You are using my site but also the sites which we can get FREE services. My site is actually a kind of a common gate for those sites. Please try this site and learn what it is and what you are using.


What's needed?
 

JAVAScript 1.2 is required for services of this site. The following browsers are recommended to use.
 

How to use


To input your sequence

You can use the sequence expressed with one-letter method only. (ex. GATCA, WTRAGFDE)
Please input your sequence in the text box in the upper area of this
You can input your sequence by CUT & PASTE or typing letters.
Although plain sequnece is recommended to input, there are no ploblems in almost of output Web sites. Even if you have a problem in the step of output, you can push BACK button of the browser and convert your sequences to a plain one by Plain seq command.
 

To clear your sequence in the text box


To convert your sequence
 
 

To convert your sequence to a plain one. G C A¨GCA
 

To make a complementary sequence of DNA. AATC¨GATT
 

The whole sequence will be expressed by upper case. gatc¨GATC
 

The whole sequence will be expressed by lower case. GATC¨gatc

- Homology Search (BLAST) -
 

You can find out the sequences homologous to yours by BLAST search.

Automatic and mannual modes are available for BLAST search. The automatic mode utilizes the best preset parameters. You can search two biggest sequence database GenBank & EMBL.

Search with the best presets

 
 

To find the gene sequence indentical to yours.
 
 

To find the protein sequence indentical to yours.
 

To find all protein family members homologus to yours.
This command is slow.
 

To find all ESTs homologus to your PROTEIN SEQUENCE
Mannual Mode
To set all parameters by yourself.
When you use this command and want to know what the parameters are, you should to visit the homepage of NCBI's BLAST.
 

- Protein Analysis -

 
Command Note Linked site
Profiles Search domain structures ISREC ProfileScan
Patterns Search motif structures ScanProsite
SMART Search Search domain structures SMART
pI&MW calculate isoelectric point and molecular weight Compute pI/Mw tool
Hydropathy test hydrophobisity of your protein by Kyte&Dolittle method ProtScale
2nd Structure Predict 2ndary structure NNPREDICT
coiled-coil Predict if it contains coiled-coil regions COILS
Cellular Localization Predict cellular localization PSORT

-  DNA Analysis -

 
Command Note Linked site
Translate Translate DNA to protein sequence The Protein Machine
Restriction Sites search the cutting sites of restriction enzymes Webcutter
PCRPrimer give you the PCR primer sequences calculated from Tm Virtual Genome Center
ORF find ORFs ORF Finder(NCBI)
Intron/Exon predict intron/exon borders in a plain seq. Splice Site Prediction by Neural Network
Find Genes predict genes in a plain seq. (max.29168 bp!) FGENES in CCG
Transcriptional Elements predict transcriptional elements TFSEARCH


Copyright and support
 

You can make a hyper-link by FREE

This is a freeware programmed by Naohiro Inohara. However, copyrights of Web sites for output, of course, belongs to their authors. I have no concern with your result which you will get because this site is a gate only and you actually utilize other sites. You can make a contact to the author by E-mail (ino@umich.edu). You should not make a contact to technical service of University of Michigan in which is the home directory of this site. Because this homepage content is a freeware, I do not have any concern for your damages or their related staffs. Copies of these hopepage contents need the author's permission.


 
History of All-in-One & What's New?
 
 
Mar/19/1998
beta version was up-loaded
Jun/1/1998
FGENES was added
July/15/1998
The site of ProfileScan was changed. SMART was added.
July/18/1998
Finally, Ver 1.0 was released!
Aug/18/1998
BLAST-2Seq was added
Feb/15/2000
PSI BLAST was added. EMBL WU BLAST was replaced to DDBJ BLAST.

Support
 
 

Please give a your tip to ino@umich.edu



 

Known bags
 

The form of SMART sometimes does not work.


Privacy
 
I repect the privacy of users who visit this site. I am not monitoring your sequences and sites which you are using.
 

 

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