Harvard:Biophysics 101/2007/Notebook:Xiaodi Wu/2007-3-15: Difference between revisions
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'''Third step:''' | '''Third step:''' | ||
Look up SNPs at Entrez SNP (query: "10 | Look up SNPs at Entrez SNP (query: "10[CHR] AND 124210300:124210800[CHRPOS]") | ||
Two exist: | Two exist: | ||
<pre> | <pre> |
Revision as of 17:58, 13 March 2007
Input sequence:
>example1 CACCCTCGCCAGTTACGAGCTGCCGAGCCGCTTCCTAGGCTCTCTGCGAATACGGACACG CATGCCACCCACAACAACTTTTTAAAAGAATCAGACGTGTGAAGGATTCTATTCGAATTA CTTCTGCTCTCTGCTTTTATCACTTCACTGTGGGTCTGGGCGCGGGCTTTCTGCCAGCTC CGCGGACGCTGCCTTCGTCCAGCCGCAGAGGCCCCGCGGTCAGGGTCCCGCGTGCGGGGT ACCGGGGGCAGAACCAGCGCGTGACCGGGGTCCGCGGTGCCGCAACGCCCCGGGTCTGCG CAGAGGCCCCTGCAGTCCCTGCCCGGCCCAGTCCGAGCTTCCCGGGCGGGCCCCCAGTCC GGCGATTTGCAGGAACTTTCCCCGGCGCTCCCACGCGAAGC
First step: Align this sequence on NCBI Blast. The result:
>ref|NT_030059.12|Hs10_30314 Homo sapiens chromosome 10 genomic contig, reference assembly Length=44617998 Features flanking this part of subject sequence: 3895 bp at 5' side: hypothetical protein 425 bp at 3' side: HtrA serine peptidase 1 Score = 736 bits (398), Expect = 0.0 Identities = 400/401 (99%), Gaps = 0/401 (0%) Strand=Plus/Plus Query 1 CACCCTCGCCAGTTACGAGCTGCCGAGCCGCTTCCTAGGCTCTCTGCGAATACGGACACG 60 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Sbjct 42968870 CACCCTCGCCAGTTACGAGCTGCCGAGCCGCTTCCTAGGCTCTCTGCGAATACGGACACG 42968929 Query 61 CATGCCACCCACAACAACTTTTTAAAAGAATCAGACGTGTGAAGGATTCTATTCGAATTA 120 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Sbjct 42968930 CATGCCACCCACAACAACTTTTTAAAAGAATCAGACGTGTGAAGGATTCTATTCGAATTA 42968989 Query 121 CTTCTGCTCTCTGCTTTTATCACTTCACTGTGGGTCTGGGCGCGGGCTTTCTGCCAGCTC 180 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Sbjct 42968990 CTTCTGCTCTCTGCTTTTATCACTTCACTGTGGGTCTGGGCGCGGGCTTTCTGCCAGCTC 42969049 Query 181 CGCGGACGCTGCCTTCGTCCAGCCGCAGAGGCCCCGCGGTCAGGGTCCCGCGTGCGGGGT 240 |||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||| Sbjct 42969050 CGCGGACGCTGCCTTCGTCCGGCCGCAGAGGCCCCGCGGTCAGGGTCCCGCGTGCGGGGT 42969109 Query 241 ACCGGGGGCAGAACCAGCGCGTGACCGGGGTCCGCGGTGCCGCAACGCCCCGGGTCTGCG 300 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Sbjct 42969110 ACCGGGGGCAGAACCAGCGCGTGACCGGGGTCCGCGGTGCCGCAACGCCCCGGGTCTGCG 42969169 Query 301 CAGAGGCCCCTGCAGTCCCTGCCCGGCCCAGTCCGAGCTTCCCGGGCGGGCCCCCAGTCC 360 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Sbjct 42969170 CAGAGGCCCCTGCAGTCCCTGCCCGGCCCAGTCCGAGCTTCCCGGGCGGGCCCCCAGTCC 42969229 Query 361 GGCGATTTGCAGGAACTTTCCCCGGCGCTCCCACGCGAAGC 401 ||||||||||||||||||||||||||||||||||||||||| Sbjct 42969230 GGCGATTTGCAGGAACTTTCCCCGGCGCTCCCACGCGAAGC 42969270
Conclusion -- this sequence we have obtained is on chromosome 10, and there is one SNP apparent.
Second step: Look at genome browser to find where exactly this is: 10q25, bases 124210300 to 124210800 (Source: [124204783.56%3A124217283.44-r&QUERY_NUMBER=1&RID=1173811506-1957-7708633758.BLASTQ2&GOTO=124210471.01human:10:bp&rsize=1562.484999999404 clicky!]
Third step: Look up SNPs at Entrez SNP (query: "10[CHR] AND 124210300:124210800[CHRPOS]") Two exist:
1: rs11200638 [Homo sapiens] AGCTCCGCGGACGCTGCCTTCGTCC[A/G]GCCGCAGAGGCCCCGCGGTCAGGGT 2: rs2672598 [Homo sapiens] CGCCGGACTGGGGGCCCGCCCGGGA[A/G]GCTCGGACTGGGCCGGGCAGGGACT