CID is a software tool, developed to operate in the World Wide Web environment, useful for the processing of cloned DNA snippets, as well as for the identification of SSRs and the establishing of primers. It holds the functionalities of some of the main genome analysis tools that are provided online.

Just follow the steps below to analyse your data with CID.

To cite CID: PATRÍCIA D. FREITAS, DIOGO S. MARTINS, PEDRO M. GALETTI JR (2008) CID: a rapid and efficient bioinformatic tool for the detection of SSRs from genomic libraries. Molecular Ecology Resources 8 (1) , 107-108 doi:10.1111/j.1471-8286.2007.01950.x

1. Input data

There are two options of input data:
- Chromatograms archive: a ZIP file holding chromatograms. The reads will be base-called by PHRED before being screened against vectors. Choose this option if the sequences provided by the sequencing machine have low quality. Because the chromatograms are base-called this option is slower than the other one.
- Sequences in FASTA format: The sequences to be processed must be pasted in the input field. Choose this option if you judge the sequences to be processed have good quality. If you're not familiar with FASTA format, use the sample next to the input field as reference.

Input format:

IMPORTANT NOTE: the submitted archive must not contain any inner folder, i.e., when you extract the files no folder is created to hold them. Otherwise, CID will fail the processing.


2. Vectors to clip

Insert into the box below the vectors to be clipped from the input sequences. All of them must be in FASTA format. If you're not familiar with FASTA format, use the sample next to the input field as reference. Leave the box blank if you have no vectors to clip from the input sequences.


3. SSR identification parameters

These are the parameters for the MISA tool which is used for SSR identification. You may change the default values to the desired values. You can disable any parameter by filling the respective field with 0 (zero).

A) Mininum repeat number for SSRs whose motifs contain:
2 pb (dinucleotide):
6 pb (hexanucleotide):
B) Minimum number of nucleotides separating two or more SSRs in order to establish compound SSRs:

4. Primer picking parameters

The parameters below are for the PRIMER3 tool which is used for designing the primers. You may change the default values to the desired values

Primer size min :
Primer size opt :
Primer size max :
Primer Tm min :
Primer Tm opt :
Primer Tm max :
Primer GC % min :
Primer GC % max :
Salt concentration :
Tm difference for primer pairs :