Journal of Heredity Advance Access originally published online on June 9, 2008
Journal of Heredity 2008 99(6):696-698; doi:10.1093/jhered/esn044
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Computer Notes |
Mining the Bovine Genome with the "Bovine SNP Retriever"
From the Parco Tecnologico Padano, Via Einstein—Località Cascina Codazza, 26900 Lodi, Italy (Panzitta, Caprera, Williams, Lazzari, and Stella); and the National Research Council (CNR), Istituto Tecnologie Biomediche, Via Fratelli Cervi 93, 20090 Segrate (MI), Italy (Merelli and Milanesi)
Address correspondence to B. Lazzari at the address above, or e-mail: barbara.lazzari{at}tecnoparco.org.
Online resources for the bovine genome analysis are provided at the most important Web sites. Nonetheless, retrieval of single-nucleotide polymorphism (SNP)–related information is not always easy when searches must focus on complementary features. In this work, we present the Bovine SNP Retriever: a user-friendly tool for bovine SNP retrieval that also facilities the retrieval of SNP-related information within user-selected quantitative traits loci regions and reverse electronic polymerase chain reaction analysis on the bovine genome. The Bovine SNP Retriever is available at http://www.itb.cnr.it/ptp/bovine_snp_retriever/.
Information on the bovine genome and its related features is mainly available from the European Bioinformatics Institute (EBI) (http://www.ensembl.org/Bos_taurus/index.html), the National Center for Biotechnology Information (NCBI) (http://www.ncbi.nlm.nih.gov/projects/genome/guide/cow/), and the Bovine Genome Database (http://genomes.tamu.edu/bovine/) resources. Currently, these sites report data based on the Btau_3.1 genome build that was released in August 2006 by the Baylor College of Medicine (BCM), on behalf of the Bos taurus sequencing project (http://genome.gov/12512284). The NCBI dbSNP collection contains more than 2 200 000 Bos Taurus RefSNP Clusters (rs numbers) based on sequences submitted by the BCM itself and by a number of other submitters.
In this work, we present the Bovine SNP Retriever: a web facility for easy retrieval of bovine single-nucleotide polymorphism (SNP)–related information that allows searches to be centered on user-defined sequences. This bioinformatic tool was designed to provide user-friendly search interfaces and to allow direct access to preexisting information that was not easily connected. Two main features are here proposed that are novel, compared with what is offered by other web resources: the possibility to perform online reverse electronic polymerase chain reaction (re-PCR) on the bovine genome and the possibility to focus searches on user-selected quantitative traits loci (QTL) regions.
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Program Description |
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 Top Program Description The BLAST InterfaceThe SNP Search InterfaceReverse Electronic PCR on...Linking SNP and QTL...Availability and System UpdateSupplementary MaterialReferences |
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The Bovine SNP Retriever bioinformatic core structure is a MySQL database. The entire bovine SNP data set was downloaded from the NCBI and used to fill in the database tables, and a web interface based on the PHP (Hypertext Preprocessor) language was prepared to allow querying of the database. All the accessory scripts that were needed were written either in Perl or in Python. As NCBI RefSNP Clusters are often associated to more than one position in the genome, the total number of records in the database does not correspond to the total number of SNP but to the total number of chromosome positions where SNP were identified. This has to be taken into account in query outputs, where the total number of matching records, and not the number of refSNP Ids, is displayed. From the home page of the Bovine SNP Retriever Web site, links are provided to the 3 main interfaces, devoted to BLAST search, SNP search, and re-PCR.
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The BLAST Interface |
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TopProgram DescriptionThe BLAST InterfaceThe SNP Search InterfaceReverse Electronic PCR on...Linking SNP and QTL...Availability and System UpdateSupplementary MaterialReferences |
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From the BLAST page, users can blast sequences against the Bos Taurus 3.1 genome assembly. BLAST (Altschul et al. 1990) is run locally against a database composed of all the cow chromosomes (Chr1–29, ChrX, and ChrUnAll), downloaded from NCBI. Three BLAST options, corresponding to 3 stand-alone BLAST command lines, can be selected: MegaBLAST (parameters: –e 1e–30), BLASTn (parameters: –e 1e–10), and BLAST oligomer sequences (BLASTn algorithm, parameters: –e 1000 –F F –W 7). Suitable e-value cutoffs can be selected by the user. Each time a BLAST search is run, users are given the possibility to retrieve SNPs that are present in the homologous regions that are identified, and these regions can be related to the QTL information. Although the standard stand-alone BLAST output format can be retrieved, the default format is tabular. This allowed us to add columns to the output table including links to the Ensembl database and to the identified SNPs page. Links to Ensembl are focused on regions homologous to the query sequence. From here, the corresponding FASTA sequence can be easily retrieved as well as all other information contained for that region in Ensembl. Links to the SNP page lead to tables where all the SNP that are present in each homologous region identified by the BLAST search are displayed with related information. Six additional links are supplied for each SNP: to the corresponding refSNP and submitted SNP pages of the NCBI dbSNP (rsID and Submission Data columns), to the NCBI Gene database (locus_id column), to the NCBI CoreNucleotide entry of the corresponding genomic contig (Contig column), to the identified QTL page (QTLs column), and to Ensembl, focused on the SNP position (chr_pos column). Links to the Gene database and to the QTL page are provided only when the identified SNP is within a known gene locus or QTL region. Depending on the user choice, BLAST outputs can be directly displayed in a browser window, downloaded, or received by e-mail.
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The SNP Search Interface |
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TopProgram DescriptionThe BLAST InterfaceThe SNP Search InterfaceReverse Electronic PCR on...Linking SNP and QTL...Availability and System UpdateSupplementary MaterialReferences |
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The SNP Search interface allows combined searches to be performed on the whole SNP Retriever database. SNPs can be retrieved according to the chromosome, sequence interval, associated gene locus Id (NCBI Gene database identifier), NCBI RefSNP Id (rs number) and assay Id (ss number), QTL trait, function class, refSNP validation state, submitter, submitter SNP Id, and allelic variant. As each QTL trait combination can contain one or more QTL regions, the selection of specific regions can be achieved by combined queries (i.e., QTL trait and chromosome number). The SNP search page query outputs are tables, reporting all the SNPs matching the query terms, with related information and links to internal and external resources (NCBI dbSNP, Gene and CoreNucleotide databases, QTL page, and Ensembl) (supplementary figure S1, Supplementary Material online). SNP flanking regions and ratios of variant base to total coverage (i.e., number of occurrences of the variant base compared with the number of readings for that position) are also included in output tables, the latter to complement validation information that is available only for a limited number of SNP positions. Tables can be downloaded in xls format. If the number of records exceeds the ordinary Excel or OpenOffice maximum size, outputs are automatically split in more than one file.
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Reverse Electronic PCR on the Bovine Genome |
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TopProgram DescriptionThe BLAST InterfaceThe SNP Search InterfaceReverse Electronic PCR on...Linking SNP and QTL...Availability and System UpdateSupplementary MaterialReferences |
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In the re-PCR page, users can perform reverse e-PCR on the Btau_3.1 genome build. Re-PCR (Schuler 1997) is run locally by the appropriate software downloaded from the NCBI ftp site, with standard parameters: users are given the possibility to choose the maximum number of allowed mismatches and gaps. When a putative amplification fragment is detected, SNPs in the identified sequence interval are searched (and matches to QTL regions are identified) and a SNP output page is created. As for the BLAST outputs, the re-PCR outputs are presented as tables containing the chromosome position and sequence interval of the putative amplicon as well as the links to the Ensembl database and to the SNP output page.
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Linking SNP and QTL Information |
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TopProgram DescriptionThe BLAST InterfaceThe SNP Search InterfaceReverse Electronic PCR on...Linking SNP and QTL...Availability and System UpdateSupplementary MaterialReferences |
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Information for QTL traits and regions was derived from the Bovine QTL viewer and database at the Texas A&M University (http://bovineqtlv2.tamu.edu/index.html) (Polineni et al. 2006). From data available at this site, a list of QTL traits was obtained, encompassing QTL regions surrounding sequence tagged sites (STS) information. Correspondences among STS names and NCBI UniSTS identifiers and consequent positioning of UniSTSs on the cow chromosomes in base pairs were deduced from files downloaded from the NCBI ftp site. As not all the UniSTS db entries have complete position information, chromosome positions in base pairs were retrieved only for 70.4% of the QTL regions that are listed at the Texas A&M University site. As a result, a list of 519 QTL regions with matching chromosome positions was added to the Bovine SNP Retriever database. Each time a SNP is identified (by direct SNP search or by the analysis of sequence intervals identified by BLAST or re-PCR), a search is performed to verify if the retrieved SNP is within one or more QTL regions. When a match is identified, a link is put in the SNP output table to the correspondent QTL table, where full information on QTL start and end markers is given, together with links to the Texas A&M University page dedicated to the corresponding QTL region.
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Availability and System Update |
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TopProgram DescriptionThe BLAST InterfaceThe SNP Search InterfaceReverse Electronic PCR on...Linking SNP and QTL...Availability and System UpdateSupplementary MaterialReferences |
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The Bovine SNP Retriever is available online for free use at http://www.itb.cnr.it/ptp/bovine_snp_retriever. Due to the large size of the BLAST and re-PCR databases, limits have been set to prevent excessive queuing. Currently, not more than 3 BLAST and 3 re-PCR sessions can be simultaneously run, and a limit of 50 kB is set for uploadable files.
The current version of the Bovine SNP Retriever uses the bovine 3.1 genome assembly; however, the database will be updated as new versions are released and are completely processed by the NCBI and Ensemble Web sites. The BLAST and the re-PCR databases will also be upgraded, in order to ensure data consistency among the different parts of the Retriever. The consistency of external links is periodically verified by an automated procedure.
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Supplementary Material |
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TopProgram DescriptionThe BLAST InterfaceThe SNP Search InterfaceReverse Electronic PCR on...Linking SNP and QTL...Availability and System UpdateSupplementary MaterialReferences |
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Supplementary Figure 1 can be found at http://www.jhered.oxfordjournals.org/.
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Acknowledgments |
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We acknowledge Dr Raffaele Mazza for helpful critical discussions and the MUR FIRB (RBLA0332RH, RBIN064YAT) LITBIO for the Bioinformatics and computational infrastructure in the frame of the Italian Bioinformatics Network (RBPR05ZK2Z) projects.
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Footnotes |
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* These authors contributed equally to this work.
Corresponding Editor: James E. Womack
Received January 10, 2008
Accepted April 24, 2008
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References |
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TopProgram DescriptionThe BLAST InterfaceThe SNP Search InterfaceReverse Electronic PCR on...Linking SNP and QTL...Availability and System UpdateSupplementary MaterialReferences |
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Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol (1990) 215:403–410.[CrossRef][Web of Science][Medline]
Polineni P, Aragonda P, Xavier SR, Furuta R, Adelson DL. The bovine QTL viewer: a web accessible database of bovine quantitative trait loci. BMC Bioinformatics (2006) 7:283.[CrossRef][Medline]
Schuler GD. Sequence mapping by electronic PCR. Genome Res (1997) 7(5):541–550.
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