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SNP-Flankplus: SNP ID-centric retrieval for SNP flanking sequences

Cheng‐Hong Yang, Yu‐Huei Cheng, Li‐Yeh Chuang, Hsueh‐Wei Chang

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Abstract

UNLABELLED: The flanking sequences provided by dbSNP of NCBI are usually short and fixed length without further extension, thus making the design of appropriate PCR primers difficult. Here, we introduce a tool named "SNP-Flankplus" to provide a web environment for retrieval of SNP flanking sequences from both the dbSNP and the nucleotide databases of NCBI. Two SNP ID types, rs# and ss#, are acceptable for querying SNP flanking sequences with adjustable lengths for at least sixteen organisms. AVAILABILITY: This software is freely available at http://bio.kuas.edu.tw/snp-flankplus/

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UNLABELLED: The flanking sequences provided by dbSNP of NCBI are usually short and fixed length without further extension, thus making the design of appropriate PCR primers difficult. Here, we introduce a tool named "SNP-Flankplus" to provide a web environment for retrieval of SNP flanking sequences from both the dbSNP and the nucleotide databases of NCBI. Two SNP ID types, rs# and ss#, are acceptable for querying SNP flanking sequences with adjustable lengths for at least sixteen organisms. AVAILABILITY: This software is freely available at http://bio.kuas.edu.tw/snp-flankplus/

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Available abstract

UNLABELLED: The flanking sequences provided by dbSNP of NCBI are usually short and fixed length without further extension, thus making the design of appropriate PCR primers difficult. Here, we introduce a tool named "SNP-Flankplus" to provide a web environment for retrieval of SNP flanking sequences from both the dbSNP and the nucleotide databases of NCBI. Two SNP ID types, rs# and ss#, are acceptable for querying SNP flanking sequences with adjustable lengths for at least sixteen organisms. AVAILABILITY: This software is freely available at http://bio.kuas.edu.tw/snp-flankplus/

Key concepts: dbSNP, SNP, Molecular Inversion Probe, Single-nucleotide polymorphism, Genetics, Tag SNP, Computational biology, R package

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