cid: a rapid and efficient bioinformatic tool for the detection of SSRs from genomic libraries

Abstract

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 http://www.shrimp.ufscar.br/cid/index.php.

Isolation and characterization of microsatellite loci for the mud-dauber wasp Trypoxylon (Trypargilum) albitarse (Hymenoptera: Crabronidae)

“…The CID (Freitas et al, 2008) and Gene Runner 3.05 (Hastings Software Inc., Hastings, NY, USA) programs were used to search for microsatellite sequences and design primers. Polymerase chain reactions (PCRs) were performed using 250 µM of each dNTP, 2.5 mM MgCl2, 1.0 µM of each primer, 1 × BioTools buffer and 1 U of Taq DNA polymerase (BioTools, Madrid, Spain) in a final volume of 10 uL.…”

Isolation and characterization of polymorphic microsatellites in the threatened catfish Jaú, Zungaro jahu (Siluriformes, Pimelodidae)

“…Primers were designed based on the flanking sequences of the repeat in each clone using the software PRIMER3 (Rozen and Skaletsky 2000). Alternatively, the set of sequences was analyzed by the CID software (Freitas et al 2008) for both the identification of microsatellites and design of primers.…”

Isolation and characterization of fifteen polymorphic tetranucleotide microsatellites for Ichthyophis bannanicus (Gymnophiona: Ichthyophiidae)

“…For those microsatellites sequences containing adequate flanking regions, PCR primers were designed using CID software (Freitas et al 2008). From these primers, 24 produced consistent amplification of loci in eight tested individuals from Mengla population.…”