bioinfolec_5th_20070713

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bioinfolec_5th_20070713

  1. 1. • • • •
  2. 2. • • • #!/bin/bash for i in *.fasta;do echo $i ~/work/blast/blast-2.2.16/bin/blastall -p blastn -d ../yeast.nt -i ”$i” > ”$i”.result done • • •
  3. 3. • • • • • • • $ ls *.result > result_list.txt
  4. 4. • • • • $ ls *.result | wc -l 84 ls | grep .result | wc -l 84
  5. 5. • • • • $ bash blast_for.sh 1.fasta 10.fasta 101.fasta $ bash blast_for.sh | cat -n 1 1.fasta 2 10.fasta 3 101.fasta 4 103.fasta () 83 94.fasta 84 98.fasta $ bash blast_for.sh | wc -l 84
  6. 6. • • • • • • • •
  7. 7. $ curl -o search_ptk2.xml ”http://eutils.ncbi.nlm.nih.gov/entrez/ eutils/esearch.fcgi?db=gene&term=ptk2quot; search_ptk2.xml <?xml version=quot;1.0quot;?> <!DOCTYPE eSearchResult PUBLIC quot;-//NLM//DTD eSearchResult, 11 May 2002//ENquot; quot;http://www.ncbi.nlm.nih.gov/entrez/query/DTD/ eSearch_020511.dtdquot;> <eSearchResult> <Count>316</Count> <RetMax>20</RetMax> <RetStart>0</RetStart> <IdList> <Id>14083</Id> <Id>5747</Id> () <Id>515604</Id> </IdList> <TranslationSet> </TranslationSet> <TranslationStack> <TermSet> <Term>ptk2[All Fields]</Term> <Field>All Fields</Field> <Count>316</Count> <Explode>Y</Explode> </TermSet>
  8. 8. $ curl ”http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi? db=gene&term=ptk2&retstart=100&retmax=50quot; <?xml version=quot;1.0quot;?> <!DOCTYPE eSearchResult PUBLIC quot;-//NLM//DTD eSearchResult, 11 May 2002//ENquot; quot;http://www.ncbi.nlm.nih.gov/entrez/query/DTD/ eSearch_020511.dtdquot;> <eSearchResult> <Count>316</Count> <RetMax>50</RetMax> <RetStart>100</RetStart> <IdList> <Id>856680</Id> <Id>856614</Id> () <Id>852891</Id> </IdList> <TranslationSet> </TranslationSet> <TranslationStack> <TermSet> <Term>ptk2[All Fields]</Term> <Field>All Fields</Field> <Count>316</Count> <Explode>Y</Explode> </TermSet> <OP>GROUP</OP>
  9. 9. • • • • • • • •
  10. 10. http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=helpentrez.table.EntrezHelp.T7 • • http://www.ncbi.nlm.nih.gov/books/bv.fcgi? rid=helpentrez.table.EntrezHelp.T6 • • •
  11. 11. • • • • • • $ curl quot;http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi? db=gene&term=ptk2+AND+quot;Mus+musculusquot;[Organism]quot;
  12. 12. • • • •
  13. 13. • • • • • $ curl quot;http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi? db=gene&term=ptk2+AND+quot;Mus+musculusquot;[Organism]&usehistory=yquot; <?xml version=quot;1.0quot;?> <!DOCTYPE eSearchResult PUBLIC quot;-//NLM//DTD eSearchResult, 11 May 2002//ENquot; quot;http://www.ncbi.nlm.nih.gov/entrez/query/DTD/ eSearch_020511.dtdquot;> <eSearchResult> <Count>13</Count> <RetMax>13</RetMax> <RetStart>0</RetStart> <QueryKey>1</QueryKey> <WebEnv>0rdtKGPJvmRtlXPjT9S3Z6StLbOltcNdfM0ojnF1AXvNusAInpLCI5SQxCi@1FB E7E6169634720_0022SID</WebEnv> <IdList> <Id>14083</Id> <Id>19229</Id> <Id>20779</Id> <Id>14784</Id>
  14. 14. • • • $ curl quot;http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi? db=gene&WebEnv=0Q0IFEamkpGbO1XfAlRwzn8k7sqIDJt93zKq3mwj6HU-90znH2Frs9A1@ 1EDD11E969637D00_0023SID&query_key=1&retmode=xmlquot; <?xml version=quot;1.0quot;?> <!DOCTYPE eSummaryResult PUBLIC quot;-//NLM//DTD eSummaryResult, 29 October 2004//ENquot; quot;http://www.ncbi.nlm.nih.gov/entrez/query/DTD/ eSummary_041029.dtdquot;> <eSummaryResult> <DocSum> <Id>14083</Id> <Item Name=quot;Namequot; Type=quot;Stringquot;>Ptk2</Item> () </DocSum> <DocSum> <Id>19229</Id> <Item Name=quot;Namequot; Type=quot;Stringquot;>Ptk2b</Item> <Item Name=quot;Descriptionquot; Type=quot;Stringquot;>PTK2 protein tyrosine kinase 2 beta</Item> () </DocSum>
  15. 15. • $ curl quot;http://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi? dbfrom=gene&db=protein&WebEnv=0Q0IFEamkpGbO1XfAlRwzn8k7sqIDJt93zKq3mwj6H U-90znH2Frs9A1@1EDD11E969637D00_0023SID&query_key=1&rettype=xmlquot; <?xml version=quot;1.0quot;?> <!DOCTYPE eLinkResult PUBLIC quot;-//NLM//DTD eLinkResult, 11 May 2002//ENquot; quot;http:// www.ncbi.nlm.nih.gov/entrez/query/DTD/eLink_020511.dtdquot;> <eLinkResult> <LinkSet> <DbFrom>gene</DbFrom> <IdList> <Id>14083</Id> () <Id>18007</Id> </IdList> <LinkSetDb> <DbTo>protein</DbTo> <LinkName>gene_protein</LinkName> <Link> <Id>143811392</Id> </Link> <Link> <Id>123796999</Id> </Link> <Link> <Id>123796465</Id> </Link>
  16. 16. • • $ curl quot;http://eutils.ncbi.nlm.nih.gov/entrez/eutils/epost.fcgi? db=gene&id=14083,5747quot; <?xml version=quot;1.0quot;?> <!DOCTYPE ePostResult PUBLIC quot;-//NLM//DTD ePostResult, 11 May 2002//ENquot; quot;http://www.ncbi.nlm.nih.gov/entrez/query/DTD/ePost_020511.dtdquot;> <ePostResult> <QueryKey>1</QueryKey> <WebEnv>0_szB71DGWKK0z12iBm4ntJUnqZZgqTU4D0hdDlcBBLgCM6RPjwMapLeP2@1EDD7 259696A98A0_0025SID</WebEnv> </ePostResult>
  17. 17. • • • $ curl quot;http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi? db=gene&WenEnv=0_szB71DGWKK0z12iBm4ntJUnqZZgqTU4D0hdDlcBBLgCM6RPjwMapLe P2@1EDD7259696A98A0_0025SID&query_key=1&retmode=xml <?xml version=quot;1.0quot;?> <!DOCTYPE eSummaryResult PUBLIC quot;-//NLM//DTD eSummaryResult, 29 October 2004//ENquot; quot;http://www.ncbi.nlm.nih.gov/entrez/query/DTD/ eSummary_041029.dtdquot;> <eSummaryResult> <DocSum> <Id>5747</Id> () </DocSum> <DocSum> <Id>14083</Id> () </DocSum>
  18. 18. • • • • • • • •
  19. 19. • • • • • • • • • •
  20. 20. • • • elink.fcgi? dbfrom=gene&db=protein&retmode=xml&WebEnv=....& query_key=... •

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