init example

sphinx/examples/blastExample

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+mkdir test.project && cd test.project
+mkdir 00.blastdb && cd 00.blastdb
+
+## copy or create symbolic links to protein sequences in 00.proteins
+cat - > ex.fasta << 'EOF'
+>gi|6850311|gb|AAF29388.1|AC009999_8 Contains similarity to a vacuolar sorting receptor homolog from Arabidopsis thaliana gb|U79959 [Arabidopsis thaliana]
+MSLPPFTCRLLAAAAALYLIGLLCVGADTKDVTAPKIPGCSNEFQMVKVENWVNGENGETFTAMTAQFGT
+MLPSDKDKAVKLPVALTTPLDSCSNLTSKLSWSIALSVRGECAFTVKAQVAQAGGAAALVLINDKEELDE
+MVCGEKDTSLNVSIPILMITTSSGDALKKSIMQNKKVELLLYAPKSPIVDDSCSNLSVGTVFVASVW
+SHVTSPKKNDEQYDELSPKKSSNVDATKGGAEEETLDISAMGAVIFVISASTFLVLLFFFMSSWFILILT
+IFFVIGGMQGMHNINVTLITRRCSKCGQKNLKLPLLGNTSILSLVVLLFCFVVAILWFMNRKTSHAWAGQ
+DIFGICMMINVLQVARLPNIRVATILLCCAFFYDIFWVFISPLIFKQSVMIAVARGSKDTGESIPMLLRI
+PRLSDPWGGYNMIGFGDILFPGLLICFIFRFDKENNKGVSNGYFPWLMFGYGLGLFLTYLGLYVMNGHGQ
+PALLYLVPCTLGITVILGLVRKELRDLWNYGTQQPSAADVNPSPEA
+
+>gi|4850398|gb|AAD31068.1|AC007357_17 Strong similarity to gi|3313615 F21J9.9 from Arabidopsis thaliana and is a member of the PF|00067 Cytochrome P450 family [Arabidopsis thaliana]
+MSEISSSMPLTERVYNHLCLSDVSLALLGLFVFCCVREKVTKKLGPTIWPVFGITPEFFFHRNDVYGWAT
+RCLKKCRGTFLYNGIWLGGSYGAVTCVPANVEYMLKTNFKNFPKGAFFKERFNDLLEDGIFNADAESWKE
+QRRIIITEMHSTRFVEHSFQTTQDLVRKKLLKVMESFARSQEAFDLQDVLLRLTFDNICIAGLGDDPGTL
+DSDLPLVPFAQAFEEATESTMFRFMIPPFIWKPLKFFDIGYEKGLRKAVDVSMSLSTRWLWIVSASSKKK
+EQSHKTTDEKDPSTIKFFRQFCTSFILAGRDTSSVALTWFFWVIQKHPEVENKIIREISEILRQRGDSPT
+SKNESLFTVKELNDMVYLQAALSETMRLYPPIPMEMKQAIEDDVFPDGTFIRKGSRVYFATYAMGRMESI
+WGKDCESFKPERWIQSGNFVNDDQFKYVVFNAGPRLCLGKTFAYLQMKTIAASVLSRYSIKVAKDHVVVP
+RVTTTLYMRHGLKVTISSKSLEEKIHVQD
+
+>gi|4850394|gb|AAD31064.1|AC007357_13 Identical to gb|X97864 cytochrome P450 from Arabidopsis thaliana and is a member of the PF|00067 Cytochrome P450 family. ESTs gb|T44875, gb|T04814, gb|R65111, gb|T44310 and gb|T04541 come from this gene [Arabidopsis thaliana]
+MSILLCFLCLLPVFLVSLSILSKRLKPSKWKLPPGPKTLPIIGNLHNLTGLPHTCFRNLSQKFGPVMLLH
+FGFVPVVVISSKEGAEEALKTQDLECCSRPETVATRMISYNFKDIGFAPYGEEWKALRKLVVMELLNTKK
+FQSFRYIREEENDLLIKKLTESALKKSPVNLKKTLFTLVASIVCRLAFGVNIHKCEFVDEDNVADLVNKF
+EMLVAGVAFTDFFPGVGWLVDRISGQNKTLNNVFSELDTFFQNVLDDHIKPGRQVSENPDVVDVMLDLMK
+KQEKDGESFKLTTDHLKGIISDIFLAGVNTSAVTLNWAMAELIRNPRVMKKVQDEIRTTLGDKKQRITEQ
+DLSQVHYFKLVVKEIFRLHPAAPLLLPRETMSHVKIQGYDIPVKTQMMINIYSIARDPKLWTNPDEFNPD
+RFLDSSIDYRGLNFELLPFGSGRRICPGMTLGITTVELGLLNLLYFFDWVVPVGKNVKDINLEETGSIII
+SKKTTLELVPLVHH
+EOF
+
+## Create blast db 
+formatdb -i ex.fasta -p T 
+
+mkdir ../10.fasta && cd ../10.fasta
+
+## Generate query files
+cat - > query1.fasta << 'EOF'
+>query1
+LLAAAAALYLIGLLCVGADKDVTAPKIPGCSNEFQMVKVEWVNGENGETFTAMTAQFGT
+MLPSDKDKAVKLPVALTTLDSCSNLTSKLSWSIALSVRGECAFTVKAQVAQAGG
+EOF
+
+cat - > query2.fasta << 'EOF'
+>query2
+KCRGTFLYNGIWLGGSYGAVTCVPANVEYMLTSSVALTWFFWVQKHPPVEVENKIIREISEILRQRGDS
+EOF
+
+## Using formatdb from older blast version
+## makeblastdb -in refseq_protein –input_type blastdb -dbtype prot
+
+mkdir ../20.blast && cd ../20.blast
+
+## Create new moa blast template
+moa new blast -t "demo run"
+
+## Define blast database location
+moa set db=../00.blastdb/ex.fasta
+
+## Define input sequence(s) location
+moa set input=../10.fasta/*.fasta
+
+## Define blast application to use
+moa set program=blastp
+
+
+## List template variables
+moa show
+
+## 
+moa run
+