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APMicroDB: A microsatellite database of Acyrthosiphon pisum

View Article: PubMed Central - PubMed

ABSTRACT

Pea aphids represent a complex genetic system that could be used for QTL analysis, genetic diversity and population genetics studies. Here, we described the development of first microsatellite repeat database of the pea aphid (APMicroDB), accessible at “http://deepaklab.com/aphidmicrodb”. We identified 3,40,233 SSRs using MIcroSAtellite (MISA) tool that was distributed in 14,067 (out of 23,924) scaffold of the pea aphid. We observed 89.53% simple repeats of which 73.41% were mono-nucleotide, followed by di-nucleotide repeats. This database stored information about the repeats kind, GC content, motif type (mono - hexa), genomic location etc. We have also incorporated the primer information derived from Primer3 software of the 2504 bp flanking region of the identified marker. Blast tool is also provided for searching the user query sequence for identified marker and their primers. This work has an immense use for scientific community working in the field of agricultural pest management, QTL mapping, and host-pathogen interaction analysis.

No MeSH data available.


Showing the database search page and its results along with primer information.
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f0015: Showing the database search page and its results along with primer information.

Mentions: We provided the scaffold wise search option for STRs along with the marker properties such as the type of motif, repeat kind etc. Furthermore, we have also given the advanced search option to filter the results based on the scaffold region, copy number of the marker, and GC content. This will be helpful to the user interested in locating the marker in the given genomic region of the genome, which may be coding or non-coding. The search result is shown in a well-organized tabular format with an additional button for extracting primer information of a particular SSR (Fig. 3). On clicking the show primer button, users will get the information about the primers (250 bp flanking region of marker) and their properties.


APMicroDB: A microsatellite database of Acyrthosiphon pisum
Showing the database search page and its results along with primer information.
© Copyright Policy - CC BY-NC-ND
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC5384296&req=5

f0015: Showing the database search page and its results along with primer information.
Mentions: We provided the scaffold wise search option for STRs along with the marker properties such as the type of motif, repeat kind etc. Furthermore, we have also given the advanced search option to filter the results based on the scaffold region, copy number of the marker, and GC content. This will be helpful to the user interested in locating the marker in the given genomic region of the genome, which may be coding or non-coding. The search result is shown in a well-organized tabular format with an additional button for extracting primer information of a particular SSR (Fig. 3). On clicking the show primer button, users will get the information about the primers (250 bp flanking region of marker) and their properties.

View Article: PubMed Central - PubMed

ABSTRACT

Pea aphids represent a complex genetic system that could be used for QTL analysis, genetic diversity and population genetics studies. Here, we described the development of first microsatellite repeat database of the pea aphid (APMicroDB), accessible at “http://deepaklab.com/aphidmicrodb”. We identified 3,40,233 SSRs using MIcroSAtellite (MISA) tool that was distributed in 14,067 (out of 23,924) scaffold of the pea aphid. We observed 89.53% simple repeats of which 73.41% were mono-nucleotide, followed by di-nucleotide repeats. This database stored information about the repeats kind, GC content, motif type (mono - hexa), genomic location etc. We have also incorporated the primer information derived from Primer3 software of the 2504 bp flanking region of the identified marker. Blast tool is also provided for searching the user query sequence for identified marker and their primers. This work has an immense use for scientific community working in the field of agricultural pest management, QTL mapping, and host-pathogen interaction analysis.

No MeSH data available.