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#!/bin/bash
for i in *.fasta;do
echo $i
~/work/blast/blast-2.2.16/bin/blastall -p blastn -d ../yeast.nt
-i ”$i” > ”$i”.result
done
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$ ls *.result > result_list.txt

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$ ls *.result | wc -l
84
ls | grep .result | wc -l
84

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$ 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

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9. $ 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>

10. $ 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>

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13. http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=helpentrez.table.EntrezHelp.T7
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• http://www.ncbi.nlm.nih.gov/books/bv.fcgi?
rid=helpentrez.table.EntrezHelp.T6
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$ curl quot;http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?
db=gene&term=ptk2+AND+quot;Mus+musculusquot;[Organism]quot;

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$ 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>

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$ 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>

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$ 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>

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$ 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>

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$ 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>

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• elink.fcgi?
dbfrom=gene&db=protein&retmode=xml&WebEnv=....&
query_key=...
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