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SSRome Genomic Pipeline
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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 analysis your uploaded data,
See Manual
,
SSRome Upload Files
.
Project Information
Analysis Name
Email
Sequence Information
Sequence with annotation information (Genbanke 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
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.
Parameters
*SSR Mining Parameters*
Mono ≥
Di ≥
Tri ≥
Tetra ≥
Penta ≥
Hexa ≥
*SSR Classification Options*
Classify SSR repeats to genic and intergenic.
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 intergenic regions.
Determine the SSR repeats unique to intergenic regions.
Note: This option to determine the SSR repeats found in intergenic regions and not found in genic regions.
Determine the SSR repeats overlapped between genic and intergenic regions.
Note: This option to determine the SSR repeats found in both genic and intergenic 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 intergenic 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
Min
Opt
Max
Primer Tm
Min
Opt
Max
Primer GC%
Min
Opt
Max
Product Size Ranges
Size
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
Comment
Thank you for use SSRome Genomic Pipeline
You will receive an email notification from SSRome Genomic Pipeline when your analysis complete.