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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.


UniPrimer input interface and main screen. (a) Main menu, (b) search result pages, (c) type of input sequence, (d) direct input of a sequence, (e) sequence upload from a file, (f) sequence position within the query sequence, (g) adding extra 5′ and 3′ sequences from the query, (h) genome assembly and their identity percentage, (i) Target locus default and user defined values.
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fig2: UniPrimer input interface and main screen. (a) Main menu, (b) search result pages, (c) type of input sequence, (d) direct input of a sequence, (e) sequence upload from a file, (f) sequence position within the query sequence, (g) adding extra 5′ and 3′ sequences from the query, (h) genome assembly and their identity percentage, (i) Target locus default and user defined values.

Mentions: The screenshot of the input interface for UniPrimer is shown on Figure 2. The main menu is located on the top right corner of the figure (Figure 2a) where the user can find information about tools, contacts, and a tutorial. The topmost tabs (Figure 2b) in the main screen are pages that will contain search results for each step after a query sequence is submitted. After selecting the type of query sequence and its assembly (Figure 2c), the user pastes the target sequence directly into text area (Figure 2d) or uploads it from a file (Figure 2e). The position (Figure 2f) option can be used if the user wants to limit the query to a specific chromosome or region. In contrast, it is also possible to add extra sequences at the 5′ and 3′ ends of the query sequence (Figure 2g). Next go the genome types, their assembly versions, and identity percentages (Figure 2h) where up to six-genome assembly similarities are searched at once. The last option in the input form is selecting the target locus (Figure 2i) in which user can select either default values (+500, −500) or define the positions that the PCR product should contain.


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)

UniPrimer input interface and main screen. (a) Main menu, (b) search result pages, (c) type of input sequence, (d) direct input of a sequence, (e) sequence upload from a file, (f) sequence position within the query sequence, (g) adding extra 5′ and 3′ sequences from the query, (h) genome assembly and their identity percentage, (i) Target locus default and user defined values.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
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fig2: UniPrimer input interface and main screen. (a) Main menu, (b) search result pages, (c) type of input sequence, (d) direct input of a sequence, (e) sequence upload from a file, (f) sequence position within the query sequence, (g) adding extra 5′ and 3′ sequences from the query, (h) genome assembly and their identity percentage, (i) Target locus default and user defined values.
Mentions: The screenshot of the input interface for UniPrimer is shown on Figure 2. The main menu is located on the top right corner of the figure (Figure 2a) where the user can find information about tools, contacts, and a tutorial. The topmost tabs (Figure 2b) in the main screen are pages that will contain search results for each step after a query sequence is submitted. After selecting the type of query sequence and its assembly (Figure 2c), the user pastes the target sequence directly into text area (Figure 2d) or uploads it from a file (Figure 2e). The position (Figure 2f) option can be used if the user wants to limit the query to a specific chromosome or region. In contrast, it is also possible to add extra sequences at the 5′ and 3′ ends of the query sequence (Figure 2g). Next go the genome types, their assembly versions, and identity percentages (Figure 2h) where up to six-genome assembly similarities are searched at once. The last option in the input form is selecting the target locus (Figure 2i) in which user can select either default values (+500, −500) or define the positions that the PCR product should contain.

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.