dbSNP flanking sequences

Question

[goyal.shiwali]

dbSNP has removed the flanking sequences of SNPs. Kindly let me know from where I can get the flanking sequences?

Answer 1

[Pierre Lindenbaum]

they're still here in the XML dumps

$ wget -q -O - "ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606_b151_GRCh38p7/XML/ds_ch1.xml.gz" | gunzip -c | grep Seq5 -m20 | cut -c 1-100
            <Seq5>ACTAATTTACAGTCCCAACAACAGTGTAAAAGTGTTCCTATTTCTCCATATCCTCTCCAGCACCTGTTGTTTCCTGACTTTT
                <Seq5>ACTAATTTACAGTCCCAACAACAGTGTAAAAGTGTTCCTATTTCTCCATATCCTCTCCAGCACCTGTTGTTTCCTGAC
                <Seq5>ACTAATTTACCCTCCCACCAACTGTGTAAAAGCATTCCTATTTCTCCACATCCTCTCCAGCCACTCTTGTATCCTGAC
                <Seq5>TCCTCTCCAGCACCTGTTGTTTCCTGACTTTTTAATGATCACCATTCTAACTGTTGCGAGATGGTATCTCATTGTGGT
            <Seq5>GACGTGGAAAATTGAGATGGATTCCCCATCTCTTCCCCAAGCCTCACTAAAACAGGAAGGAATGGAAAGTGACCTAAGTGAC
                <Seq5>TGCACCAGATCTTTACCCTCTGGGGGGCTGAATCAACGAGTNCTAGACTGAAGCACCCAGGCACAGCCAAGGGTGAGG
                <Seq5>GACGTGGAAAATTGAGATGGATTCCCCATCTCTTCCCCAAGCCTCACTAAAACAGGAAGGAATGGAAAGTGACCTAAG
                <Seq5>TGAGGGAGCCATGATCCTGAACATAGCATTGACTGATTAATGAGACCCCC</Seq5>
                <Seq5>TGAGGGAGCCATGATCCTGAACATAGCATTGACTGATTAATGAGACCCCC</Seq5>
                <Seq5>GCATTGACTGATTAATGAGACCCCC</Seq5>
                <Seq5>GCATTGACTGATTAATGAGACCCCC</Seq5>
                <Seq5>GCATTGACTGATTAATGAGACCCCC</Seq5>
                <Seq5>GCATTGACTGATTAATGAGACCCCC</Seq5>
                <Seq5>GCATTGACTGATTAATGAGACCCCC</Seq5>
                <Seq5>GCATTGACTGATTAATGAGACCCCC</Seq5>
                <Seq5>GCATTGACTGATTAATGAGACCCCC</Seq5>
                <Seq5>GCATTGACTGATTAATGAGACCCCC</Seq5>
                <Seq5>GCATTGACTGATTAATGAGACCCCC</Seq5>
                <Seq5>GCATTGACTGATTAATGAGACCCCC</Seq5>
                <Seq5>GCATTGACTGATTAATGAGACCCCC</Seq5>