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2019 blast Practice example
The location where gene prediction of pearl Exoc 7 seems to be wrong estimated from closely related species
First of all file preparation
echo ">exoc7_pearl atgactctgaaggatgccctcaacaaaagtcacacaaatacaggaaacatgctcacaata cttcaaagctttgaaaatcgtttaaagaagttagagggaacagttgagcctgtttacaat gagacagaaatgctgcggcgcagacaagaaaatatagagaaaactatgacaacactggac aatgtgctgggttactaccatattgctaaagatgtacaagatttgattaaagaaggtcca gtagtttgtggtctggagaagtacctgtctactatggaccggctgctccaagcactgaac tactttaataaacataacccaaccagtctggaagtgacagatgtcatcaaagtatatgat gatggtaaagatacattgaatgcagagttccgtagtttacttggtcgtcactgtcgtccg gtgccggctgttactatactggatttactaggaccagatgaagagttacaaacaatggaa aatgatgcacccatagaacatctgcctgagaaaattgtgaatgatttaaccctcatcgca aagtggctatacaccaatggtaaagctacagagtatatgaaagattacaccaaagtcagg tcccaaatgctcctctactctctgcaggggaactcaataaagcggaaggctaccacggcc ttgatgcagtccccttttgatccaggtcatagaagacaaggctcttataacgaattgaca aaagaggaaagttttgatgttgaaattgatatctacataacagaactaacagcattgctg aaacttattcagaatgaccctgagagatcttcgatgccccgagacggtacagttcatgaa ctgacaaaccataccattatagtactggagcccctgttagattatgctgagacagctggg gccatgttactcacccatggtgaacatgcagttccatctgatgctgtggatgtcaagaaa agtaaactcaagttggctgactatatcactaaggttttgtcagcattaggattaaactta agtaacaaggcagaaacttacagtgatccaatactcagacatgtgttcatgcttaataac tatcactacatactcaagtctttaaaaaggtctggggtattagaattaattcacacatgg aataaagatgtaggacagttttatgaggaccagatacatgaacaaaaaagactttattcc cagagctggagtaaagttctacattttgtactggaaatgaatgagccaatatcccaacaa agaatccagcaaatggagacatcaaagataaaggacaaagaaaagcagaatataaaagac aagttctctggattcaacaaagagttggaagaaatctcacgtgttcagaaagcatacgcc attcctgatccagaactgagggacaatatcaagaaagacaataaagaatatattgtgccg cgatacaagcttttcttagaaaaatttcaacggctgaacttcacaaagaattcagaaaaa tatatgaaatacactgtaaaggatgtggaagaaacacttgataaatttttcgatacttca gcttaa" > exoc7_pearl.fna
echo ">EKC30356.1 Exocyst complex component 7 [Crassostrea gigas] MLTILQSFENRLRKLENTVEPVYNETEMLRRRQENIEKTMVTLDNVLGYYHVGKEVEEFIKEGPHNCGLE KYLSIMDRLVQAHNYFNKHNPTSLELTDVIRVYDDGKEALVIEFRTLLGRHCRPVPPVMVLDMISTDEEL QGSDDIQLEHLPEKILTELSLISTWLFNNTKNTEYMKDYTRSRSSMLIKSLQGHSFKRRAVITLMQSPFD PGNKRQGSHAELPKEENLDVEVDIYITELSALLKLIQSEAQLMSGIIADKHHRSVFDNIIQEGLDSVIKN GELLAVNAKKSIAKHDFINVLSVFPVLKHLRSIKPEFDLTLEGCATPTRAKLTSLLSTLGSTAAKALEEF ALSIKTDPEKASMPKDGTVHELTNRTIIFLEPLQDYADTAGAMLLLHGEQAAPSEAVDPKKSKMRLADYI TKTLSALGLNLTIKAETYSDPTLRPVFMLNNYHYILKSLKRSGLLDLIHTWNKDVGQFYEDRINEQKKLY SESWSRVMHYITEVHEPISQQRIQAMENSKLKDKEKQNIKDKFSGFNKELEDILKIQKGYAIPDPELREQ MKKDNKDFIIPAFRMFLDKFKRLNFTKNPEKYIKYSVQDVAEVVDKLFDMSA" > exoc7_c.gigas.faa
Download the genome of the pearl oyster which you will use later.
wget https://marinegenomics.oist.jp/pearl/download/pfu_genome1.0.fasta.gz gzip -d pfu_genome1.0.fasta.gz
When you're ready, start docker to set up an environment that uses blast.
docker run -it --rm -v $PWD:$PWD -w $PWD quay.io/biocontainers/blast:2.7.1--boost1.64_1 bash
Entering the above commands will enter the virtual environment available to blast. The amino acid sequence of exoc7_c.gigas is used as a DB, and the nucleotide sequence of exoc7_pearl is used as a query. First, create a database of exoc7_c.gigas.
makeblastdb -in exoc7_c.gigas.faa -dbtype prot