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UniPrimer: A Web-Based Primer Design Tool for Comparative Analyses of Primate Genomes.

Batnyam N, Lee J, Lee J, Hong SB, Oh S, Han K - Comp. Funct. Genomics (2012)

Bottom Line: UniPrimer is linked to RepeatMasker, Primer3Plus, and OligoCalc softwares to produce primers with high accuracy and UCSC In-Silico PCR to confirm whether the designed primers work.To test the performance of UniPrimer, we designed primers on sample sequences using UniPrimer and manually designed primers for the same sequences.The comparison of the two processes showed that UniPrimer was more effective than manual work in terms of saving time and reducing errors.

View Article: PubMed Central - PubMed

Affiliation: Department of Nanobiomedical Science and WCU Research Center, Dankook University, Cheonan 330-714, Republic of Korea.

ABSTRACT
Whole genome sequences of various primates have been released due to advanced DNA-sequencing technology. A combination of computational data mining and the polymerase chain reaction (PCR) assay to validate the data is an excellent method for conducting comparative genomics. Thus, designing primers for PCR is an essential procedure for a comparative analysis of primate genomes. Here, we developed and introduced UniPrimer for use in those studies. UniPrimer is a web-based tool that designs PCR- and DNA-sequencing primers. It compares the sequences from six different primates (human, chimpanzee, gorilla, orangutan, gibbon, and rhesus macaque) and designs primers on the conserved region across species. UniPrimer is linked to RepeatMasker, Primer3Plus, and OligoCalc softwares to produce primers with high accuracy and UCSC In-Silico PCR to confirm whether the designed primers work. To test the performance of UniPrimer, we designed primers on sample sequences using UniPrimer and manually designed primers for the same sequences. The comparison of the two processes showed that UniPrimer was more effective than manual work in terms of saving time and reducing errors.

No MeSH data available.


Pick primer result. (a) Table showing primers, their detailed information, and position in the sequence. (b) Additional options for the Pick primer step.
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fig5: Pick primer result. (a) Table showing primers, their detailed information, and position in the sequence. (b) Additional options for the Pick primer step.

Mentions: Pick primer is linked to Primer3Plus, which selects the primer pairs that fit best to the selected parameters and orders them by quality. The Pick primer output is shown in Figure 5. The left side table (Figure 5a) will contain detailed information of all possible primers present in the query sequence, as well as the whole sequence with BLAT and RepeatMasker output results shown together; the left primers are highlighted in purple, the right primers are highlighted in yellow, the BLAT mismatches are marked in red, and the masked repeats are highlighted in light green.


UniPrimer: A Web-Based Primer Design Tool for Comparative Analyses of Primate Genomes.

Batnyam N, Lee J, Lee J, Hong SB, Oh S, Han K - Comp. Funct. Genomics (2012)

Pick primer result. (a) Table showing primers, their detailed information, and position in the sequence. (b) Additional options for the Pick primer step.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3368176&req=5

fig5: Pick primer result. (a) Table showing primers, their detailed information, and position in the sequence. (b) Additional options for the Pick primer step.
Mentions: Pick primer is linked to Primer3Plus, which selects the primer pairs that fit best to the selected parameters and orders them by quality. The Pick primer output is shown in Figure 5. The left side table (Figure 5a) will contain detailed information of all possible primers present in the query sequence, as well as the whole sequence with BLAT and RepeatMasker output results shown together; the left primers are highlighted in purple, the right primers are highlighted in yellow, the BLAT mismatches are marked in red, and the masked repeats are highlighted in light green.

Bottom Line: UniPrimer is linked to RepeatMasker, Primer3Plus, and OligoCalc softwares to produce primers with high accuracy and UCSC In-Silico PCR to confirm whether the designed primers work.To test the performance of UniPrimer, we designed primers on sample sequences using UniPrimer and manually designed primers for the same sequences.The comparison of the two processes showed that UniPrimer was more effective than manual work in terms of saving time and reducing errors.

View Article: PubMed Central - PubMed

Affiliation: Department of Nanobiomedical Science and WCU Research Center, Dankook University, Cheonan 330-714, Republic of Korea.

ABSTRACT
Whole genome sequences of various primates have been released due to advanced DNA-sequencing technology. A combination of computational data mining and the polymerase chain reaction (PCR) assay to validate the data is an excellent method for conducting comparative genomics. Thus, designing primers for PCR is an essential procedure for a comparative analysis of primate genomes. Here, we developed and introduced UniPrimer for use in those studies. UniPrimer is a web-based tool that designs PCR- and DNA-sequencing primers. It compares the sequences from six different primates (human, chimpanzee, gorilla, orangutan, gibbon, and rhesus macaque) and designs primers on the conserved region across species. UniPrimer is linked to RepeatMasker, Primer3Plus, and OligoCalc softwares to produce primers with high accuracy and UCSC In-Silico PCR to confirm whether the designed primers work. To test the performance of UniPrimer, we designed primers on sample sequences using UniPrimer and manually designed primers for the same sequences. The comparison of the two processes showed that UniPrimer was more effective than manual work in terms of saving time and reducing errors.

No MeSH data available.