Limits...
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.


The overall flow of user Blast query, and its link to database and primers.
© Copyright Policy - CC BY-NC-ND
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC5384296&req=5

f0020: The overall flow of user Blast query, and its link to database and primers.

Mentions: A customized BLAST tool is implemented in this database for similarity search. The user input query sequence will be searched against the database of repeats containing flanking region. A user-friendly search option for e-value cut off, query coverage and a number of hits to be displayed is provided in the blast search. The identified hit is further linked with the primer information of the identified hits (Fig. 4).


APMicroDB: A microsatellite database of Acyrthosiphon pisum
The overall flow of user Blast query, and its link to database and primers.
© Copyright Policy - CC BY-NC-ND
Related In: Results  -  Collection

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

f0020: The overall flow of user Blast query, and its link to database and primers.
Mentions: A customized BLAST tool is implemented in this database for similarity search. The user input query sequence will be searched against the database of repeats containing flanking region. A user-friendly search option for e-value cut off, query coverage and a number of hits to be displayed is provided in the blast search. The identified hit is further linked with the primer information of the identified hits (Fig. 4).

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.