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UgMicroSatdb: database for mining microsatellites from unigenes.

Aishwarya V, Sharma PC - Nucleic Acids Res. (2007)

Bottom Line: The database also provides information about trinucleotide repeats encoding various amino acids.Such codon repeats can be searched by specifying characteristics of coded amino acids like charge (basic, acidic or neutral), polarity (polar or non-polar), and their hydrophobic or hydrophilic nature.The nucleotide sequences of the target UniGenes are also provided to facilitate primer designing for PCR amplification of the desired microsatellite.

View Article: PubMed Central - PubMed

Affiliation: University School of Biotechnology, Guru Gobind Singh Indraprastha University, Kashmere Gate, Delhi 110 006, India.

ABSTRACT
Microsatellites, also known as simple sequence repeats (SSRs) or short tandem repeats (STRs), have extensively been exploited as molecular markers for diverse applications. Recently, their role in gene regulation and genome evolution has also been discussed widely. We have developed UgMicroSatdb (Unigene MicroSatellite database), a web-based relational database of microsatellites present in unigene sequences covering 80 genomes. UgMicroSatdb allows microsatellite search using multiple parameters like microsatellite type (simple perfect, compound perfect and imperfect), repeat unit length (mono- to hexa-nucleotide), repeat number, microsatellite length and repeat sequence class. Microsatellites can also be retrieved by specifying EST, cDNA, CDS identity or by using Gene Index, GenBank, UniGene IDs. The database also provides information about trinucleotide repeats encoding various amino acids. Such codon repeats can be searched by specifying characteristics of coded amino acids like charge (basic, acidic or neutral), polarity (polar or non-polar), and their hydrophobic or hydrophilic nature. The nucleotide sequences of the target UniGenes are also provided to facilitate primer designing for PCR amplification of the desired microsatellite. UgMicroSatdb is available at http://ipu.ac.in/usbt/UgMicroSatdb.htm.

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Data exchange flow diagram for UgMicroSatdb.
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Figure 1: Data exchange flow diagram for UgMicroSatdb.

Mentions: UgMicroSatdb provides a catalogue of microsatellites occurring in unigene sequences of eukaryotic organisms belonging to a wide range of taxonomic groups. UniGene sequences were downloaded from The National Center for Biotechnology Information (NCBI) and scanned using a simple sequence repeat mining tool called MISA (19) that extracted microsatellite motifs and wrote them in tab delimited text files. This raw microsatellite information was processed using a set of C++ codes and Perl scripts. VMI_PRCS, a C++ code, processed statistics like size and position of microsatellites within the unigene sequences. VUG_PRCS, another C++ code, processed unigene IDs and sequences in the desired format. The data was reassembled using a Perl script VDATA_ASMBL and a data file was created. The data file was further formatted and then imported as a table in a MS-ACCESS database. Similar approach was adopted for all the individual sets of unigene sequences of different species. The overall scheme of database construction is explained in Figure 1. The quick retrieval of information from UgMicroSatdb has been ensured by creating small, specific sub-databases for different groups of organisms. Furthermore, within each sub-database, individual organism has been represented by a separate table. A parent database that indexes all the sub-databases and the tables therein maintains fast, efficient and precise communication with these sub-databases. The graphical user interface was constructed using Active Server Pages (ASP). The overall architecture of the database has been outlined in Figure 2.Figure 1.


UgMicroSatdb: database for mining microsatellites from unigenes.

Aishwarya V, Sharma PC - Nucleic Acids Res. (2007)

Data exchange flow diagram for UgMicroSatdb.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2238862&req=5

Figure 1: Data exchange flow diagram for UgMicroSatdb.
Mentions: UgMicroSatdb provides a catalogue of microsatellites occurring in unigene sequences of eukaryotic organisms belonging to a wide range of taxonomic groups. UniGene sequences were downloaded from The National Center for Biotechnology Information (NCBI) and scanned using a simple sequence repeat mining tool called MISA (19) that extracted microsatellite motifs and wrote them in tab delimited text files. This raw microsatellite information was processed using a set of C++ codes and Perl scripts. VMI_PRCS, a C++ code, processed statistics like size and position of microsatellites within the unigene sequences. VUG_PRCS, another C++ code, processed unigene IDs and sequences in the desired format. The data was reassembled using a Perl script VDATA_ASMBL and a data file was created. The data file was further formatted and then imported as a table in a MS-ACCESS database. Similar approach was adopted for all the individual sets of unigene sequences of different species. The overall scheme of database construction is explained in Figure 1. The quick retrieval of information from UgMicroSatdb has been ensured by creating small, specific sub-databases for different groups of organisms. Furthermore, within each sub-database, individual organism has been represented by a separate table. A parent database that indexes all the sub-databases and the tables therein maintains fast, efficient and precise communication with these sub-databases. The graphical user interface was constructed using Active Server Pages (ASP). The overall architecture of the database has been outlined in Figure 2.Figure 1.

Bottom Line: The database also provides information about trinucleotide repeats encoding various amino acids.Such codon repeats can be searched by specifying characteristics of coded amino acids like charge (basic, acidic or neutral), polarity (polar or non-polar), and their hydrophobic or hydrophilic nature.The nucleotide sequences of the target UniGenes are also provided to facilitate primer designing for PCR amplification of the desired microsatellite.

View Article: PubMed Central - PubMed

Affiliation: University School of Biotechnology, Guru Gobind Singh Indraprastha University, Kashmere Gate, Delhi 110 006, India.

ABSTRACT
Microsatellites, also known as simple sequence repeats (SSRs) or short tandem repeats (STRs), have extensively been exploited as molecular markers for diverse applications. Recently, their role in gene regulation and genome evolution has also been discussed widely. We have developed UgMicroSatdb (Unigene MicroSatellite database), a web-based relational database of microsatellites present in unigene sequences covering 80 genomes. UgMicroSatdb allows microsatellite search using multiple parameters like microsatellite type (simple perfect, compound perfect and imperfect), repeat unit length (mono- to hexa-nucleotide), repeat number, microsatellite length and repeat sequence class. Microsatellites can also be retrieved by specifying EST, cDNA, CDS identity or by using Gene Index, GenBank, UniGene IDs. The database also provides information about trinucleotide repeats encoding various amino acids. Such codon repeats can be searched by specifying characteristics of coded amino acids like charge (basic, acidic or neutral), polarity (polar or non-polar), and their hydrophobic or hydrophilic nature. The nucleotide sequences of the target UniGenes are also provided to facilitate primer designing for PCR amplification of the desired microsatellite. UgMicroSatdb is available at http://ipu.ac.in/usbt/UgMicroSatdb.htm.

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