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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.


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Mentions: The last page of UniPrimer contains the primer information picked by the user (Figure 6). The upper part of the table shows the left and right primer sequences and their melting temperatures in Celsius. Figure 7 shows a pop-up window that the user can reach by clicking the “OligoClac” button on the Figure 6 and potential hairpin, 3′ complementarity, and self-annealing sites of candidate primers are calculated and displayed. The lower part of the table in Figure 6 shows the genome type, the genomic position, and the expected size of the PCR product. Nationally, the user can access UCSC In-Silico PCR by clicking the “Product” button on the right side of Figure 6 (Figure 8). In the results of In-Silico PCR, primers that are written in capital letters and sequences that lie between them are written in small letters (Figure 8).


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)

Oligo self-complementary check window.
© Copyright Policy
Related In: Results  -  Collection

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

fig7: Oligo self-complementary check window.
Mentions: The last page of UniPrimer contains the primer information picked by the user (Figure 6). The upper part of the table shows the left and right primer sequences and their melting temperatures in Celsius. Figure 7 shows a pop-up window that the user can reach by clicking the “OligoClac” button on the Figure 6 and potential hairpin, 3′ complementarity, and self-annealing sites of candidate primers are calculated and displayed. The lower part of the table in Figure 6 shows the genome type, the genomic position, and the expected size of the PCR product. Nationally, the user can access UCSC In-Silico PCR by clicking the “Product” button on the right side of Figure 6 (Figure 8). In the results of In-Silico PCR, primers that are written in capital letters and sequences that lie between them are written in small letters (Figure 8).

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.