SSRome Genomic Pipeline

Sequence with annotation information (Genbank format) See Example.

Separate sequence in fasta format See Example.

Note: If you select "Separate sequence in fasta format" option you could also select "Separate annotation file" option to provide annotation information of your sequence.

Separate annotation file.

Genbank File

Note: Please provide the name of Genbank File you uploaded through "SSRome Upload Files" page. Or write "None" in case of no file uploaded.

OR

Fasta File

Note: Please provide the name of Fasta File you uploaded through "SSRome Upload Files" page. Or write "None" in case of no file uploaded.

And

Annotation File

Note: Please provide the name of Annotation File you uploaded through "SSRome Upload Files" page. Or write "None" in case of no file uploaded.

Classify SSR repeats to genic and non-genic.

Note: If you didn't feed SSRome Genomic Pipeline with your annotation information, please don't select this option.

Determine the SSR repeats unique to genic regions.

Note: This option to determine the SSR repeats found in genic regions and not found in non-genic regions.

Determine the SSR repeats unique to non-genic regions.

Note: This option to determine the SSR repeats found in non-genic regions and not found in genic regions.

Determine the SSR repeats shared between genic and non-genic regions.

Note: This option to determine the SSR repeats found in both genic and non-genic regions.

Design SSR primers in genic regions.

Note: If you didn't feed SSRome Genomic Pipeline with your annotation information, please don't select this option.

Design SSR primers in non-genic regions.

Note: If you didn't feed SSRome Genomic Pipeline with your annotation information, please don't select this option.

Design SSR primers in all genomic regions.

Note: select this option if you didn't feed SSRome Genomic Pipeline with annotation information.

Compare your SSR repeats with SSRome Database.

Note1: select this option if you want to compare your results (identified SSR repeats) with SSRome Database to determine the unique repeats to your organism.

Note2: If you selected this option you should provide SSRome Comparative Analysis Pipeline with your organism scientific name.Or write "None" if you don't select this option.

Store your results in SSRome database.

* Store your results in SSRome database and make it available free online.

Don't store my results in SSRome database.

* If you agree to Store your results in SSRome database, please provide us the date you want make it available free online

Available free online date

Comment

SSRome Genomic Pipeline

Note: To use SSRome Genomic Pipeline you should upload all your data/files at first, then you can use SSRome Genomic Pipeline to analyze your uploaded data, See Manual, SSRome Upload Files.

Project Information

Sequence Information

Sequence with annotation information (Genbank format) See Example.

Separate sequence in fasta format See Example.

Note: If you select "Separate sequence in fasta format" option you could also select "Separate annotation file" option to provide annotation information of your sequence.

Separate annotation file.

Input Data

Note: Please provide the name of Genbank File you uploaded through "SSRome Upload Files" page. Or write "None" in case of no file uploaded.

OR

Note: Please provide the name of Fasta File you uploaded through "SSRome Upload Files" page. Or write "None" in case of no file uploaded.

And

Note: Please provide the name of Annotation File you uploaded through "SSRome Upload Files" page. Or write "None" in case of no file uploaded.

Parameters

*SSR Mining Parameters*

*SSR Classification Options*

Classify SSR repeats to genic and non-genic.

Note: If you didn't feed SSRome Genomic Pipeline with your annotation information, please don't select this option.

Determine the SSR repeats unique to genic regions.

Note: This option to determine the SSR repeats found in genic regions and not found in non-genic regions.

Determine the SSR repeats unique to non-genic regions.

Note: This option to determine the SSR repeats found in non-genic regions and not found in genic regions.

Determine the SSR repeats shared between genic and non-genic regions.

Note: This option to determine the SSR repeats found in both genic and non-genic regions.

*SSR primer design options*

Design SSR primers in genic regions.

Note: If you didn't feed SSRome Genomic Pipeline with your annotation information, please don't select this option.

Design SSR primers in non-genic regions.

Note: If you didn't feed SSRome Genomic Pipeline with your annotation information, please don't select this option.

Design SSR primers in all genomic regions.

Note: select this option if you didn't feed SSRome Genomic Pipeline with annotation information.

Primer size

Primer Tm

Primer GC%

Product Size Range

SSRome Comparative Analysis

Compare your SSR repeats with SSRome Database.

Note1: select this option if you want to compare your results (identified SSR repeats) with SSRome Database to determine the unique repeats to your organism.

Note2: If you selected this option you should provide SSRome Comparative Analysis Pipeline with your organism scientific name.Or write "None" if you don't select this option.

Your organism scientific name

SSRome Genomic Pipeline Results

Availability of SSRome Genomic Pipeline Results

Store your results in SSRome database.

* Store your results in SSRome database and make it available free online.

Don't store my results in SSRome database.

* If you agree to Store your results in SSRome database, please provide us the date you want make it available free online

Available free online date

Thank you for use SSRome Genomic Pipeline

You will receive an email notification from SSRome Genomic Pipeline when your analysis complete.

SSR Mining Parameters

SSR Classification Options

SSR primer design options