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find identical sequences with different header

I have two fasta file with 200 sequences. I want to use shell commands to find identical sequences with different headers between theses two fasta files and save that in new file with heder as output.

forexample: 

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

new file:

>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
sequence
• 3,185 views • link
updated by GenoMax GenoMax • written by Jason • Jason

Hello,

this code will work : seqkit common --by-seq --ignore-case file1.fasta file2.fasta > out.fasta

but it displays there is only one match sequence and will save all sequence from file1 in out.file

I only want to save match sequences, so result will be :

>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
• 0 views • link
updated by GenoMax GenoMax • written by Jason • Jason

Jason : Please use ADD COMMENT/ADD REPLY when responding to existing posts to keep threads logically organized.

• 0 views • link
written by GenoMax GenoMax

2 answers

Dear Jason,

our SEDA software (http://www.sing-group.org/seda/) has an option to remove and report duplicated sequences.

It is described in section 3.4 "Remove redundant sequences" of the user manual (http://www.sing-group.org/seda/downloads/manuals/seda-user-manual-1.0.0.pdf). If you check the "Save merged headers into a file" you will be able to select a file where the headers corresponding to redundant sequences are reported. This option also allows you to look for subsequences, that is, sequences contained into other sequences.

Regards,

Hugo.

• 0 views • link
written by Hugo Hugo

i don't want to remove duplicate sequences. I want to save duplicate sequences from two files and save result in new file

• 0 views • link
written by Jason • Jason 
seqkit common --by-seq --ignore-case file1.fasta file2.fasta file3.fasta > out.fasta

Download binaries for Linux/Windows/Mac OS X, usage

• 0 views • link
written by shenwei356 shenwei356

Hello,

this code will work :

seqkit common --by-seq --ignore-case file1.fasta file2.fasta > out.fasta

but it displays there is only one match sequence and will save all sequence from file1 in out.file

I only want to save match sequences, so result will be :

>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
• 0 views • link
updated by GenoMax GenoMax • written by Jason • Jason

The result indeed is the >NP_000009.1. Don't you check the out.fasta?

• 0 views • link
written by shenwei356 shenwei356

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