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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.


BLAT search results. Matching and mismatching bases are in black and red, respectively.
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fig3: BLAT search results. Matching and mismatching bases are in black and red, respectively.

Mentions: BLAT step allows a user to find orthologous between a query sequence and several other genomes. A BLAT search result is shown in Figure 3. Identical bases between the query sequence and its corresponding sequences from other primates are colored black but mismatches between sequences are all combined and marked as red letters. However, below it, user can find links to a detailed comparison of a query sequence with each of selected genomes, separately.


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)

BLAT search results. Matching and mismatching bases are in black and red, respectively.
© Copyright Policy
Related In: Results  -  Collection

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

fig3: BLAT search results. Matching and mismatching bases are in black and red, respectively.
Mentions: BLAT step allows a user to find orthologous between a query sequence and several other genomes. A BLAT search result is shown in Figure 3. Identical bases between the query sequence and its corresponding sequences from other primates are colored black but mismatches between sequences are all combined and marked as red letters. However, below it, user can find links to a detailed comparison of a query sequence with each of selected genomes, separately.

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.