I have two fasta file with 200 sequences. I want to use shell commands to find difference sequences with different headers between theses two fasta files and save that in new file with heder from file as output.
this command find match sequences even if header is not same. it look at match sequences and skip header.
seqkit common --by-seq --ignore-case file1.fasta file2.fasta file3.fasta > out.fasta
I want to find difference sequences from file 1 not find in file 2 and save that in file 3. we want to compare by sequences not header becasue both file have different header but some sequences same and other are different.
file1:
>NP_000009.1 very long-chain specific acyl-CoA dehydrogenase, mitochondrial isoform 1 precursor [Homo sapiens]
MQAARMAASLGRQLLRLGGGSSRLTALLGQPRPGPARRPYAGGAAQLALDKSDSHPSDALTRKKPAKAES
KSFAVGMFKGQLTTDQVFPYPSVLNEEQTQFLKELVEPVSRFFEEVNDPAKNDALEMVEETTWQGLKELG
AFGLQVPSELGGVGLCNTQYARLVEIVGMHDLGVGITLGAHQSIGFKGILLFGTKAQKEKYLPKLASGET
VAAFCLTEPSSGSDAASIRTSAVPSPCGKYYTLNGSKLWISNGGLADIFTVFAKTPVTDPATGAVKEKIT
AFVVERGFGGITHGPPEKKMGIKASNTAEVFFDGVRVPSENVLGEVGSGFKVAMHILNNGRFGMAAALAG
TMRGIIAKAVDHATNRTQFGEKIHNFGLIQEKLARMVMLQYVTESMAYMVSANMDQGATDFQIEAAISKI
FGSEAAWKVTDECIQIMGGMGFMKEPGVERVLRDLRIFRIFEGTNDILRLFVALQGCMDKGKELSGLGSA
LKNPFGNAGLLLGEAGKQLRRRAGLGSGLSLSGLVHPELSRSGELAVRALEQFATVVEAKLIKHKKGIVN
EQFLLQRLADGAIDLYAMVVVLSRASRSLSEGHPTAQHEKMLCDTWCIEAAARIREGMAALQSDPWQQEL
YRNFKSISKALVERGGVVTSNPLGF
>NP_000010.1 acetyl-CoA acetyltransferase, mitochondrial precursor [Homo sapiens]
MAVLAALLRSGARSRSPLLRRLVQEIRYVERSYVSKPTLKEVVIVSATRTPIGSFLGSLSLLPATKLGSI
AIQGAIEKAGIPKEEVKEAYMGNVLQGGEGQAPTRQAVLGAGLPISTPCTTINKVCASGMKAIMMASQSL
MCGHQDVMVAGGMESMSNVPYVMNRGSTPYGGVKLEDLIVKDGLTDVYNKIHMGSCAENTAKKLNIARNE
QDAYAINSYTRSKAAWEAGKFGNEVIPVTVTVKGQPDVVVKEDEEYKRVDFSKVPKLKTVFQKENGTVTA
ANASTLNDGAAALVLMTADAAKRLNVTPLARIVAFADAAVEPIDFPIAPVYAASMVLKDVGLKKEDIAMW
EVNEAFSLVVLANIKMLEIDPQKVNINGGAVSLGHPIGMSGARIVGHLTHALKQGEYGLASICNGGGGAS
AMLIQKL
file2:
>sp|Q8R519|ACMSD_MOUSE 2-amino-3-carboxymuconate-6-semialdehyde decarboxylase OS=Mus musculus GN=Acmsd PE=1 SV=2
MKIDIHTHILPKEWPDLEKRFGYGGWVQLQQQGKGEAKMIKDGKLFRVIQQNCWDPEVRI
REMNQKGVTVQALSTVPVMFSYWAKPKDTLELCQFLNNDLAATVARYPRRFVGLGTLPMQ
APELAVEEMERCVKALGFPGIQIGSHINTWDLNDPELFPIYAAAERLNCSLFVHPWDMQM
DGRMAKYWLPWLVGMPSETTMAICSMIMGGVFEKFPKLKVCFAHGGGAFPFTIGRIAHGF
NMRPDLCAQDNPSDPRKYLGSFYTDSLVHDPLSLKLLTDVIGKDKVMLGTDYPFPLGEQE
PGKLIESMAEFDEETKDKLTAGNALAFLGLERKLFE
>sp|P35738|ODBB_RAT 2-oxoisovalerate dehydrogenase subunit beta, mitochondrial OS=Rattus norvegicus GN=Bckdhb PE=1 SV=3
MQAARMAASLGRQLLRLGGGSSRLTALLGQPRPGPARRPYAGGAAQLALDKSDSHPSDALTRKKPAKAES
KSFAVGMFKGQLTTDQVFPYPSVLNEEQTQFLKELVEPVSRFFEEVNDPAKNDALEMVEETTWQGLKELG
AFGLQVPSELGGVGLCNTQYARLVEIVGMHDLGVGITLGAHQSIGFKGILLFGTKAQKEKYLPKLASGET
VAAFCLTEPSSGSDAASIRTSAVPSPCGKYYTLNGSKLWISNGGLADIFTVFAKTPVTDPATGAVKEKIT
AFVVERGFGGITHGPPEKKMGIKASNTAEVFFDGVRVPSENVLGEVGSGFKVAMHILNNGRFGMAAALAG
TMRGIIAKAVDHATNRTQFGEKIHNFGLIQEKLARMVMLQYVTESMAYMVSANMDQGATDFQIEAAISKI
FGSEAAWKVTDECIQIMGGMGFMKEPGVERVLRDLRIFRIFEGTNDILRLFVALQGCMDKGKELSGLGSA
LKNPFGNAGLLLGEAGKQLRRRAGLGSGLSLSGLVHPELSRSGELAVRALEQFATVVEAKLIKHKKGIVN
EQFLLQRLADGAIDLYAMVVVLSRASRSLSEGHPTAQHEKMLCDTWCIEAAARIREGMAALQSDPWQQEL
YRNFKSISKALVERGGVVTSNPLGF
>sp|P26149|3BHS2_MOUSE 3 beta-hydroxysteroid dehydrogenase/Delta 5-->4-isomerase type 2 OS=Mus musculus GN=Hsd3b2 PE=1 SV=4
MPGWSCLVTGAGGFLGQRIIQLLVQEEDLEEIRVLDKVFRPETRKEFFNLETSIKVTVLE
GDILDTQYLRRACQGISVVIHTAAIIDVTGVIPRQTILDVNLKGTQNLLEACIQASVPAF
IFSSSVDVAGPNSYKEIVLNGHEEECHESTWSDPYPYSKKMAEKAVLAANGSMLKNGGTL
QTCALRPMCIYGERSPLISNIIIMALKHKGILRSFGKFNTANPVYVGNVAWAHILAARGL
RDPKKSPNIQGEFYYISDDTPHQSFDDISYTLSKEWGFCLDSSWSLPVPLLYWLAFLLET
VSFLLSPIYRYIPPFNRHLVTLSGSTFTFSYKKAQRDLGYEPLVSWEEAKQKTSEWIGTL
VEQHRETLDTKSQ
result file 3
>NP_000010.1 acetyl-CoA acetyltransferase, mitochondrial precursor [Homo sapiens]
MAVLAALLRSGARSRSPLLRRLVQEIRYVERSYVSKPTLKEVVIVSATRTPIGSFLGSLSLLPATKLGSI
AIQGAIEKAGIPKEEVKEAYMGNVLQGGEGQAPTRQAVLGAGLPISTPCTTINKVCASGMKAIMMASQSL
MCGHQDVMVAGGMESMSNVPYVMNRGSTPYGGVKLEDLIVKDGLTDVYNKIHMGSCAENTAKKLNIARNE
QDAYAINSYTRSKAAWEAGKFGNEVIPVTVTVKGQPDVVVKEDEEYKRVDFSKVPKLKTVFQKENGTVTA
ANASTLNDGAAALVLMTADAAKRLNVTPLARIVAFADAAVEPIDFPIAPVYAASMVLKDVGLKKEDIAMW
EVNEAFSLVVLANIKMLEIDPQKVNINGGAVSLGHPIGMSGARIVGHLTHALKQGEYGLASICNGGGGAS
AMLIQKL