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Extracting known SNPs

 

 

Search for known SNPs in a given sequence in NCBI database.

Output example:

Sequences producing significant alignments:
gnl|dbSNP|rs1409128	rs=1409128|pos=301|len=601|taxid=9606|mol="cDNA"|class=1|alleles="A /C"|build=130|score(bits)=624
gnl|dbSNP|rs1409127	rs=1409127|pos=301|len=601|taxid=9606|mol="cDNA"|class=1|alleles="C /T"|build=126|score(bits)=624

gnl|dbSNP|rs17553802	rs=17553802|pos=274|len=452|taxid=9606|mol="cDNA"|class=1|alleles=" C/T"|build=123|score(bits)=575
gnl|dbSNP|rs3215811	rs=3215811|pos=404|len=452|taxid=9606|mol="cDNA"|class=2|alleles="- /A"|build=126|score(bits)=575
gnl|dbSNP|rs34136598	rs=34136598|pos=301|len=601|taxid=9606|mol="cDNA"|class=1|alleles=" C/T"|build=126|score(bits)=167
gnl|dbSNP|rs6573036	rs=6573036|pos=514|len=2741|taxid=9606|mol="cDNA"|class=1|alleles="A/ G"|build=130|score(bits)=159
gnl|dbSNP|rs4901588	rs=4901588|pos=2448|len=2741|taxid=9606|mol="cDNA"|class=1|alleles="C /T"|build=129|score(bits)=159
gnl|dbSNP|rs4901587	rs=4901587|pos=2394|len=2741|taxid=9606|mol="cDNA"|class=1|alleles="C /T"|build=129|score(bits)=159

gnl|dbSNP|rs2296544	rs=2296544|pos=61|len=121|taxid=9606|mol="cDNA"|class=1|alleles="C/ T"|build=100|score(bits)=149
>gnl|dbSNP|rs1409128 rs=1409128|pos=301|len=601|taxid=9606|mol="cDNA"|class=1|alleles="A /C"|build=130 Length = 347 Score = 624 bits (315), Expect = 1e-175 Identities = 336/347, (96%) Strand = Plus/Plus; Query: 1-347; Sbjct: 77-423; Query: 1 tcactgacatttcctaattaaccaagttctgccaagtttcacatgaaacttggggaaccg Sbjct: 77 ............................................................ Query: 61 atttcattcccccagtatcaccctgtggcgccaccttccggagctgtgaggaaactccgg Sbjct: 137 ............................................................ Query: 121 acttccccccaacaccgccccctccctccaccctcggtctccgctttctgcgctctgccg Sbjct: 197 ............................................................ Query: 181 cgttggttttcggaggtgtctgggcgcatgcgctttggacgggccgcctagcctaggaga Sbjct: 257 ............................................m............... Query: 241 gactacaattcccagaagacagtgcgaaagnnnnnnnnnntcccgcggtccgtgggggtg Sbjct: 317 ..............................aaaaaaaaaa.................... Query: 301 ggagaaataaacgctcgcgagagaacgaggttcaggcggctgcacga Sbjct: 377 ...............................................
>gnl|dbSNP|rs1409127 rs=1409127|pos=301|len=601|taxid=9606|mol="cDNA"|class=1|alleles="C /T"|build=126 Length = 347 Score = 624 bits (315), Expect = 1e-175 Identities = 336/347, (96%) Strand = Plus/Plus; Query: 1-347; Sbjct: 221-567; Query: 1 tcactgacatttcctaattaaccaagttctgccaagtttcacatgaaacttggggaaccg Sbjct: 221 ............................................................ Query: 61 atttcattcccccagtatcaccctgtggcgccaccttccggagctgtgaggaaactccgg Sbjct: 281 ....................y....................................... Query: 121 acttccccccaacaccgccccctccctccaccctcggtctccgctttctgcgctctgccg Sbjct: 341 ............................................................ Query: 181 cgttggttttcggaggtgtctgggcgcatgcgctttggacgggccgcctagcctaggaga Sbjct: 401 ............................................................ Query: 241 gactacaattcccagaagacagtgcgaaagnnnnnnnnnntcccgcggtccgtgggggtg Sbjct: 461 ..............................aaaaaaaaaa.................... Query: 301 ggagaaataaacgctcgcgagagaacgaggttcaggcggctgcacga Sbjct: 521 ...............................................
>gnl|dbSNP|rs17553802 rs=17553802|pos=274|len=452|taxid=9606|mol="cDNA"|class=1|alleles=" C/T"|build=123 Length = 328 Score = 575 bits (290), Expect = 1e-161 Identities = 316/328, (96%) Strand = Plus/Plus; Query: 1-328; Sbjct: 124-452; Query: 1 tcactgacatttcctaattaaccaagttctgccaagtttcacatgaaacttggggaaccg Sbjct: 124 ............................................................ Query: 61 atttcattcccccagtatcaccctgtggcgccaccttccggagctgtgaggaaactccgg Sbjct: 184 ............................................................ Query: 121 acttccccccaacaccgccccctccctccaccctcggtctccgctttctgcgctctgccg Sbjct: 244 ..............................y............................. Query: 181 cgttggttttcggaggtgtctgggcgcatgcgctttggacgggccgcctagcctaggaga Sbjct: 304 ............................................m............... Query: 241 gactacaattcccagaagacagtgcgaaagnnnnnnnnnn-tcccgcggtccgtgggggt Sbjct: 364 ..............................aaaaaaaaaan................... Query: 301 gggagaaataaacgctcgcgagagaacg Sbjct: 424 ............................
>gnl|dbSNP|rs3215811 rs=3215811|pos=404|len=452|taxid=9606|mol="cDNA"|class=2|alleles="- /A"|build=126 Length = 328 Score = 575 bits (290), Expect = 1e-161 Identities = 316/328, (96%) Strand = Plus/Plus; Query: 1-328; Sbjct: 124-452; Query: 1 tcactgacatttcctaattaaccaagttctgccaagtttcacatgaaacttggggaaccg Sbjct: 124 ............................................................ Query: 61 atttcattcccccagtatcaccctgtggcgccaccttccggagctgtgaggaaactccgg Sbjct: 184 ............................................................ Query: 121 acttccccccaacaccgccccctccctccaccctcggtctccgctttctgcgctctgccg Sbjct: 244 ..............................y............................. Query: 181 cgttggttttcggaggtgtctgggcgcatgcgctttggacgggccgcctagcctaggaga Sbjct: 304 ............................................m............... Query: 241 gactacaattcccagaagacagtgcgaaagnnnnnnnnnn-tcccgcggtccgtgggggt Sbjct: 364 ..............................aaaaaaaaaan................... Query: 301 gggagaaataaacgctcgcgagagaacg Sbjct: 424 ............................
>gnl|dbSNP|rs34136598 rs=34136598|pos=301|len=601|taxid=9606|mol="cDNA"|class=1|alleles=" C/T"|build=126 Length = 202 Score = 167 bits (84), Expect = 7e-38 Identities = 175/202, (85%) Strand = Plus/Plus; Query: 431-632; Sbjct: 360-558; Query: 431 ggtttgtatccgggctgtgaggtgctcggagcctcggcggaccttgctgcctctgtctct Sbjct: 360 ......g....a....a.........g........a.ta..a...t..........t... Query: 491 ttaacgcgagaggaagcgatgcagaggggtggaaaatggcagagctgcagatgttactag Sbjct: 420 ....t..a.......c....a....a.................................. Query: 551 aggaggagatcccgtctggcaagagggcgctgatcgagagttaccagaacctga-ctcgg Sbjct: 480 .....-.--...t....ca.........a.....a...................a.-.a. Query: 611 gtggcaga-ctactgtgaaaac Sbjct: 540 .....-..a..........g..
>gnl|dbSNP|rs6573036 rs=6573036|pos=514|len=2741|taxid=9606|mol="cDNA"|class=1|alleles="A/ G"|build=130 Length = 174 Score = 159 bits (80), Expect = 2e-35 Identities = 151/174, (86%) Strand = Plus/Plus; Query: 431-604; Sbjct: 2571-2741; Query: 431 ggtttgtatccgggctgtgaggtgctcggagcctcggcggaccttgctgcctctgtctct Sbjct: 2571 ......g....a....a.........g........a.ta..a...t..........t... Query: 491 ttaacgcgagaggaagcgatgcagaggggtggaaaatggcagagctgcagatgttactag Sbjct: 2631 ....t..a.......c....a....a.................................. Query: 551 aggaggagatcccgtctggcaagagggcgctgatcgagagttaccagaacctga Sbjct: 2691 .....-.--...t....ca.........a.....a...................
>gnl|dbSNP|rs4901588 rs=4901588|pos=2448|len=2741|taxid=9606|mol="cDNA"|class=1|alleles="C /T"|build=129 Length = 174 Score = 159 bits (80), Expect = 2e-35 Identities = 151/174, (86%) Strand = Plus/Plus; Query: 431-604; Sbjct: 2561-2731; Query: 431 ggtttgtatccgggctgtgaggtgctcggagcctcggcggaccttgctgcctctgtctct Sbjct: 2561 ......g....a....a.........g........a.ta..a...t..........t... Query: 491 ttaacgcgagaggaagcgatgcagaggggtggaaaatggcagagctgcagatgttactag Sbjct: 2621 ....t..a.......c....a....a.................................. Query: 551 aggaggagatcccgtctggcaagagggcgctgatcgagagttaccagaacctga Sbjct: 2681 .....-.--...t....ca.........a.....a...................
>gnl|dbSNP|rs4901587 rs=4901587|pos=2394|len=2741|taxid=9606|mol="cDNA"|class=1|alleles="C /T"|build=129 Length = 174 Score = 159 bits (80), Expect = 2e-35 Identities = 151/174, (86%) Strand = Plus/Plus; Query: 431-604; Sbjct: 2561-2731; Query: 431 ggtttgtatccgggctgtgaggtgctcggagcctcggcggaccttgctgcctctgtctct Sbjct: 2561 ......g....a....a.........g........a.ta..a...t..........t... Query: 491 ttaacgcgagaggaagcgatgcagaggggtggaaaatggcagagctgcagatgttactag Sbjct: 2621 ....t..a.......c....a....a.................................. Query: 551 aggaggagatcccgtctggcaagagggcgctgatcgagagttaccagaacctga Sbjct: 2681 .....-.--...t....ca.........a.....a...................
>gnl|dbSNP|rs2296544 rs=2296544|pos=61|len=121|taxid=9606|mol="cDNA"|class=1|alleles="C/ T"|build=100 Length = 77 Score = 149 bits (75), Expect = 2e-32 Identities = 76/77, (98%) Strand = Plus/Plus; Query: 394-470; Sbjct: 45-121; Query: 394 tgccgtcccacaataccaggcgggagggcgggtaggcggtttgtatccgggctgtgaggt Sbjct: 45 ................y........................................... Query: 454 gctcggagcctcggcgg Sbjct: 105 .................

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