CID: A rapid and efficient bioinformatic tool for the detection of SSRs from genomic libraries

Departamento de Genética e Evolução, Universidade Federal de São Carlos, Via Washington Luiz km 235, Caixa Postal 676, CEP 13565-905, São Carlos, SP, Brazil.
Molecular Ecology Resources (Impact Factor: 3.71). 01/2008; 8(1):107-8. DOI: 10.1111/j.1471-8286.2007.01950.x
Source: PubMed


cid is a computational tool developed in the Web environment to process cloned DNA fragments with the objective of masking the vector and adaptor regions, detecting the presence of microsatellites and designing the most appropriate primer pairs for the amplification of the identified repetitive sequences. This entire process is executed by the user in a simple and automated manner with the data input as a Zip file of chromatograms or a multiFASTA file. Thus, it is possible to analyse dozens of sequences at the same time, optimizing data processing and the search for the information of interest. cid is freely available on

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Available from: Patrícia Domingues de Freitas, Apr 16, 2015
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    • "The cloned inserts from 96 recombinant plasmids were sequenced on an ABI3730XL by the Sanger dideoxi-terminator method by Macrogen (South Korea). Microsatellites were localized using the software CID (Freitas et al. 2008). Identification and removal of sequences related to the adapters and cloning vector was done using VecScreen (http://www.ncbi.nlm. "
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    ABSTRACT: Ten microsatellite loci were isolated and characterized from the spiny-rat (Clyomy bishopi), a mediumsize Neotropical rodent that inhabits some of the last remaining savannas from Sa˜o Paulo state, Brazil. Between 5 and 17 alleles were detected per locus, with expected heterozygosity ranging from 0.605 to 0.921. All but one locus were found to be in Hardy–Weinberg equilibrium, and no linkage disequilibrium was detected among pairs of loci. These microsatellites should provide useful markers in genetic studies including parentage analyses and determining genetic and social structure of populations.
    Full-text · Article · Oct 2012 · Conservation Genetics Resources
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    • "For the microsatellites sequences containing adequate flanking regions, PCR primers were designed using CID software [5]. From these primers, 28 produced consistent amplification of loci in eight tested individuals from Yong’an population. "
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    ABSTRACT: We characterize thirteen polymorphic microsatellite loci isolated from Naja atra genomic libraries, which were enriched for AC-motif microsatellites. The thirteen loci were screened on a group of 48 individuals from two populations, one in Yong'an and the other in Ganzhou. These markers revealed a relatively high degree of genetic diversity (4-12 alleles per locus) and heterozygosity (Ho ranged from 0.213-0.854 and He ranged from 0.301-0.838). Tests for departure from Hardy-Weinberg equilibrium and for linkage disequilibrium were conducted for each of the two populations separately. After sequential Bonferroni correction, none of the 13 loci showed significant departures from Hardy-Weinberg equilibrium. Hierarchical analysis of molecular variance indicated that a small but significant (P < 0.001) proportion (16.0%) of the total variation in the microsatellite DNA data were attributable to differences among populations, indicating geographical structuring and restricted gene flow. It could be attributable to the Wuyi mountains in the area having a sufficiently isolating effect to significantly reduce gene flow. Our microsatellite data also showed a low N(m) (1.31) value in the two populations from mainland China. Thus, the Yong'an and Ganzhou populations could be treated as distinct evolutionarily significant units (ESUs). The high level of polymorphism revealed by these microsatellite markers will be useful for the study of gene flow, population structure and evolutionary history of N. atra.
    Full-text · Article · Dec 2011 · International Journal of Molecular Sciences
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    • "Enriched DNA was cloned using the pGem-T Easy Vector (Promega) and 96 clones were sequenced in an ABI3730XL automated sequencer. The sequences were analyzed using the CID program (Freitas et al. 2008) for microsatellite identification and design of the primers. Nineteen microsatellites were identified and their primers were constructed using a 5 0 18 base pair M13 universal sequence strategy (Schuelke 2000) for indirect fluoro-labeling detection. "
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    ABSTRACT: Dendrocincla turdina has a poor ability to survive in fragmented areas and inhabits the depleted Brazilian Atlantic Forest. For the assessment of genetic diversity in this species, nineteen microsatellite loci were isolated and characterized, 11 of which were polymorphic for the population studied. Observed and expected heterozigosity ranged from 0.07 to 0.80 and 0.08 to 0.91, respectively. Cross-amplification was successfully obtained with two other species from the family Dendrocolaptidae: Xiphorhynchus fuscus and Sittasomus griseicapillus. The newly developed primers reported here constitute a useful tool for genetic population analyses on D. turdina and, potentially, other related species. KeywordsGenetic conservation-Passeriformes-Atlantic forest-Population genetics
    Full-text · Article · Jan 2011 · Conservation Genetics Resources
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