SSRome ManualSSRome Main-Bar Overview

 Home: Navigation Bar; About SSRome; SSRome Genomic Pipeline; SSRome
Transcriptomic Pipeline; SSRome Comparative Analysis Pipeline; Analyzed Genomes
in SSRome Database; Analyzed ESTs in SSRome Database; Analyzed Organelle
Genome’s in SSRome Database; Valuable Resources, Useful Links; How to cite.
 SSRome Database: Statistics; Download; Database Search; SSRome Comparisons.
 SSRome Pipelines: SSRome Upload Files; SSRome Genomic Pipeline; SSRome
Transcriptomic Pipeline; SSRome Comparative Analysis Pipeline.
 Manual Contact

Home Page About SSRomeHome Page
 SSRome Genomic Pipeline

 SSRome TranscriptomicPipeline

 SSRome Comparative
Analysis Pipeline

Home Page
 Analyzed Genomes in SSRome Database

Select one of thisgenra
Organism ScientificName

Click to go to theOrganism SpecificSearch Page
* the Organism Specific Search Page Layout

Home Page

 Analyzed ESTs in SSRome Database Analyzed Organelles Genomes in SSRome Database

Clickto thePage
Organism
SearchPage
Click to go
to tothegoSearchfor eachcategory

Clickto thePage
Organism
SearchPage
Click to go
to tothegoSearchfor eachcategory

Statistics Pageto toview
plant
MoveClickfrom oneanother
Genra by“Click”
to view
statistics
table
Genomic
Statistics
statistics
tablepart

Categories
Click toStatistics
view plantstatistics tableDownload Page

Click to view all analyzed Plant results
available in SSRome
Genomic download part

Click to view all analyzed Metazoa results
available in SSRome

Click to view all Others organisms results
available in SSRome
Organelles download part

Transcriptomic download part

Download Page

Download the SSR repeats found in genic regions and not found in Non-genic regions

Download the SSR motifs found inboth genic and non-genic regions

Download genic-SSR repeats statistics
Download all genic-SSR repeats

Download all genic-SSR primers

Download all non-genic SSR repeats

Download all non-genic SSR primers

Download non-genic SSR repeats statistics

Download the SSR repeats found in non- genic regions
and not found in genic regions

Search Page

Move from one to another Search
Page by “Click”* the Plant Search Page Layout

Click toStatistics
Searchview plant
Categories
Categories
statistics table

Search Page

Please enter (write) the Gene Symbol or Locus
Tag of sequence you looking for. “Optional”

Please enter the SSRome primer-Id
in Primer Id field "Optional"
Please enter (write) the repeat sequence
you looking for. “Optional”
Please select the organism name from
Organism Name drop down menu

Please select SSR repeat type from
Repeat Type drop down menu

Comparisons Page
Please select SSR repeat type from
Repeat Type drop down menu

Move from one to another Genra
Comparisons Page by “Click”

Search for SSR motifs overlapped
between genic and non-genic regions
View genic SSR motifs statistics
View non-genic SSR motifs statistics
View SSR unique motifs to genic regions

View SSR unique motifs to non-genicregions

Please select theorganism name fromOrganism Name dropdown menu

SSRome Upload Files page

For “huge sized file(s)” please create the SSRome
FTP account "available for free“ .

For “small sized file(s)” select file from yourcomputer and click “upload”

For “huge sized files”, We suggest to use one of
the following tools to upload your files.

SSRome Genomic Pipeline page (Part-1)

Enter your analysis nameEnter your Email address to notify you
when your analysis complete.

“Check” to customize youranalysis parameters

SSRome Genomic Pipeline page (Part-2)
Enter the name of Genbank File you uploaded through"SSRome Upload Files" page. Or write "None" in caseof no file uploaded.
Enter the name of Fasta File you uploaded through"SSRome Upload Files" page. Or write "None" in caseof no file uploaded.
Enter the name of Annotation File you uploaded
through "SSRome Upload Files" page. Or write"None" in case of no file uploaded.
Customize SSR Mining Parameters“Check” to customize your SSR
classification parameters

Customize your SSR primer designoptions

SSRome Genomic Pipeline page (Part-3)
Select this option if you want to compare yourresults (identified SSR repeats) with SSRomeDatabase to determine the unique repeats to yourorganism
If you selected previous option you should feed
SSRome Comparative Analysis Pipeline with yourorganism scientific name. Or write "None" if you
don't select this option.

Customize your SSRome Genomic Pipeline
Results options
If you agree to Store your results in
SSRome database, please provide us thedate you want to make it available freely
onlineEnter your comment(S)Click “submit” to run your analysis

SSRome Transcriptomic Pipeline (Part-1)

Enter your analysis nameEnter your Email address to notify you
when your analysis complete.

“Check” to customize youranalysis parameters

SSRome Transcriptomic Pipeline (Part-2)
In the case your transcriptome (RNA-Seq) sample
without annotation, Please enter the file name you
uploaded through "SSRome Upload Files" page. Or
write "None" in case of no file uploaded

In the case your transcriptome (RNA-Seq) sample withannotation, Please enter the file name you uploaded
through "SSRome Upload Files" page. Or write "None"in case of no file uploaded

Customize SSR Mining Parameters

Customize your SSR primer designParameters“Check” to customize yourannotation analysis parameters

SSRome Transcriptomic Pipeline (Part-3)

Customize your SSRome Transcriptomic
Pipeline Results options
If you agree to Store your results inSSRome database, please provide us thedate you want to make it available freely
onlineEnter your comment(S)Click “submit” to run your analysis

SSRome Comparative Analysis Pipeline (Part-1)

Enter your analysis nameEnter your Email address to notify you
when your analysis complete.

“Check” to customize youroptions

SSRome Comparative Analysis Pipeline (Part-2)
Enter your organism scientific nameEnter the name of SSR repeat file you uploaded
through "SSRome Upload Files" page. Or write "None"in case of no file uploaded.
Enter the name of Genbank file you uploaded through"SSRome Upload Files" page. Or write "None" in caseof no file uploaded.
Customize SSR Mining Parameters
Enter the SSR Mining tool name used todetermine the SSR repeats
Customize your SSRome Transcriptomic
Pipeline Results options
If you agree to Store your results in
SSRome database, please provide us thedate you want to make it available freelyonline
Enter your comment(S)Click “submit” to run your analysis

For any further questions please contact us