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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.


RepeatMasker search result. (a) Detailed annotation of repeats in a table format. (b) Sequence format with masked repeats; masked areas are highlighted in light green. (c) Extra options for selecting the target locus and primer type. (d) Separate tables summarize repetitive elements found in each of selected primate genomes (orthologous region).
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fig4: RepeatMasker search result. (a) Detailed annotation of repeats in a table format. (b) Sequence format with masked repeats; masked areas are highlighted in light green. (c) Extra options for selecting the target locus and primer type. (d) Separate tables summarize repetitive elements found in each of selected primate genomes (orthologous region).

Mentions: RepeatMasker helps to eliminate the building of any candidate primer containing repetitive elements by masking them. Primers that are built on unmasked areas are more successful than those built on masked areas. The output result of RepeatMasker (Figure 4) returns a detailed annotation of repeat elements that are present in the query sequence. The annotation is shown in two formats; a table format contains a list of the repeats (Figure 4a), and repeat sequences are highlighted with light green color in the other format (Figure 4b). On the right side of the window, the user can find options to change the target locus and the type of primer (Figure 4c). After selecting the options, the user obtains a list of designed primers by clicking “Pick primer” on the top right corner of the main screen (step C-3 in Figure 1). Under the masked sequence, there are separate tables that describe masked areas of 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)

RepeatMasker search result. (a) Detailed annotation of repeats in a table format. (b) Sequence format with masked repeats; masked areas are highlighted in light green. (c) Extra options for selecting the target locus and primer type. (d) Separate tables summarize repetitive elements found in each of selected primate genomes (orthologous region).
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Related In: Results  -  Collection

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

fig4: RepeatMasker search result. (a) Detailed annotation of repeats in a table format. (b) Sequence format with masked repeats; masked areas are highlighted in light green. (c) Extra options for selecting the target locus and primer type. (d) Separate tables summarize repetitive elements found in each of selected primate genomes (orthologous region).
Mentions: RepeatMasker helps to eliminate the building of any candidate primer containing repetitive elements by masking them. Primers that are built on unmasked areas are more successful than those built on masked areas. The output result of RepeatMasker (Figure 4) returns a detailed annotation of repeat elements that are present in the query sequence. The annotation is shown in two formats; a table format contains a list of the repeats (Figure 4a), and repeat sequences are highlighted with light green color in the other format (Figure 4b). On the right side of the window, the user can find options to change the target locus and the type of primer (Figure 4c). After selecting the options, the user obtains a list of designed primers by clicking “Pick primer” on the top right corner of the main screen (step C-3 in Figure 1). Under the masked sequence, there are separate tables that describe masked areas of 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.