SB Map features prot2nucl

--map_features_prot2nucl, -fp2n

Description

Transfer protein feature annotations onto their corresponding nucleotide sequences. The nucleotide and amino acid files must be separate.

SeqBuddy will throw a warning if it finds sequences in either file that are not also present in the other, but this can be silenced with the -q flag.

Examples

Input file 1: Mle-Panxα4_pep.gb

LOCUS       Mle-Panxα4               425 aa                     UNA 02-JAN-2015
DEFINITION  cDNA and genomic - ML129317a.
ACCESSION   Mle-Panxα4
VERSION     Mle-Panxα4
KEYWORDS    .
SOURCE
  ORGANISM  . . . .
            .
FEATURES             Location/Qualifiers
     TMD1            28..48
     TMD2            131..151
     TMD3            215..235
     TMD4            305..335
ORIGIN
        1 mviellagyk glspfkdatv ddswdqinrc yvfiamvvmg avttmrqysg tliacdgftk
       61 fhpqfaedyc wsigmytvre aydlpssmva ypgvipwdmp acvprllkng trtkcgsekd
      121 vmpsekiyhl wyqwasfyfw ivailyyapy imfkqlggge ykplikllcl asgspeqqmq
      181 diqervvkwl ffrfktyifa kgyyawlrkn sfsiaigvtk lsyllitilv fyltgfmfey
      241 gsntwyryga dwygtrfssy hetnnsitlt kdiifpkmva ceikrwgpsg ievetaqcvl
      301 apnvlyqylf lftwylliav fftnliscfl hisemffsng tynrmidqgm lpdkpsyryv
      361 fmnigaggre ivqiltdnsn pllfskifdd ltnllittsk nadvienlsk ldssvielgs
      421 kdsi*
//

Input file 2: Mle-Panxα4_mrna.fa

>Mle-Panxα4 cDNA and genomic - ML129317a.
AUGGUUAUUGAGCUGCUAGCUGGAUACAAAGGUCUGUCCCCGUUUAAAGACGCGACUGUU
GACGACUCAUGGGACCAAAUAAACCGAUGUUACGUGUUCAUCGCCAUGGUGGUGAUGGGU
GCUGUGACUACAAUGAGGCAAUACUCUGGAACAUUGAUUGCAUGUGACGGGUUCACGAAG
UUCCACCCUCAGUUUGCAGAAGAUUACUGCUGGAGCAUAGGAAUGUACACGGUACGCGAG
GCCUAUGACUUGCCCAGCAGUAUGGUUGCAUACCCCGGAGUGAUACCCUGGGAUAUGCCU
GCAUGUGUUCCACGUCUCCUGAAGAACGGAACCAGGACCAAAUGUGGCAGUGAGAAGGAC
GUUAUGCCCUCAGAGAAAAUCUACCACUUGUGGUACCAGUGGGCAAGUUUCUACUUCUGG
AUAGUGGCUAUACUGUACUACGCGCCGUAUAUAAUGUUCAAACAGUUGGGAGGGGGAGAG
UACAAGCCCCUGAUCAAGCUACUUUGUCUUGCGUCUGGAUCUCCUGAACAACAGAUGCAG
GACAUCCAGGAGCGUGUCGUCAAGUGGCUUUUCUUCAGGUUUAAGACCUACAUAUUCGCU
AAGGGUUACUACGCGUGGCUACGUAAAAACAGUUUCAGUAUCGCUAUCGGCGUGACAAAA
UUGUCCUAUCUCCUGAUAACUAUCCUUGUGUUCUACUUAACAGGCUUCAUGUUCGAAUAU
GGCUCUAACACGUGGUACCGGUACGGUGCUGACUGGUACGGUACCAGAUUCUCCUCGUAC
CACGAAACUAACAACUCAAUCACACUCACAAAGGACAUCAUCUUCCCAAAGAUGGUAGCG
UGUGAGAUCAAGCGAUGGGGUCCCUCAGGGAUUGAGGUUGAGACCGCUCAGUGCGUACUU
GCCCCGAAUGUGCUCUACCAGUACCUUUUCCUCUUUACUUGGUACCUCCUGAUCGCGGUA
UUCUUCACUAACCUCAUCAGUUGUUUCCUCCACAUUUCUGAGAUGUUCUUCUCUAACGGU
ACGUACAACAGGAUGAUAGAUCAAGGAAUGUUGCCAGACAAGCCCAGUUAUCGGUACGUC
UUCAUGAACAUUGGCGCCGGUGGCAGAGAGAUAGUCCAGAUUCUAACAGACAAUUCCAAC
CCCCUCUUGUUUAGCAAGAUAUUUGACGAUCUUACCAAUUUACUAAUCACUACUUCCAAA
AACGCUGACGUCAUUGAAAACCUGUCGAAGUUGGAUUCCUCCGUAAUUGAACUAGGCAGC
AAAGACUCAAUCUAA

Usage

$: sb Mle-Panxα4_mrna.fa Mle-Panxα4_pep.gb -fp2n

Output

LOCUS       Mle-Panxα4              1275 bp    RNA              UNK 01-JAN-1980
DEFINITION  Mle-Panxα4 cDNA and genomic - ML129317a.
ACCESSION   Mle-Panxα4
VERSION     Mle-Panxα4
KEYWORDS    .
SOURCE      .
  ORGANISM  .
            .
FEATURES             Location/Qualifiers
     TMD1            82..144
     TMD2            391..453
     TMD3            643..705
     TMD4            913..1005
ORIGIN
        1 augguuauug agcugcuagc uggauacaaa ggucuguccc cguuuaaaga cgcgacuguu
       61 gacgacucau gggaccaaau aaaccgaugu uacguguuca ucgccauggu ggugaugggu
      121 gcugugacua caaugaggca auacucugga acauugauug caugugacgg guucacgaag
      181 uuccacccuc aguuugcaga agauuacugc uggagcauag gaauguacac gguacgcgag
      241 gccuaugacu ugcccagcag uaugguugca uaccccggag ugauacccug ggauaugccu
      301 gcauguguuc cacgucuccu gaagaacgga accaggacca aauguggcag ugagaaggac
      361 guuaugcccu cagagaaaau cuaccacuug ugguaccagu gggcaaguuu cuacuucugg
      421 auaguggcua uacuguacua cgcgccguau auaauguuca aacaguuggg agggggagag
      481 uacaagcccc ugaucaagcu acuuugucuu gcgucuggau cuccugaaca acagaugcag
      541 gacauccagg agcgugucgu caaguggcuu uucuucaggu uuaagaccua cauauucgcu
      601 aaggguuacu acgcguggcu acguaaaaac aguuucagua ucgcuaucgg cgugacaaaa
      661 uuguccuauc uccugauaac uauccuugug uucuacuuaa caggcuucau guucgaauau
      721 ggcucuaaca cgugguaccg guacggugcu gacugguacg guaccagauu cuccucguac
      781 cacgaaacua acaacucaau cacacucaca aaggacauca ucuucccaaa gaugguagcg
      841 ugugagauca agcgaugggg ucccucaggg auugagguug agaccgcuca gugcguacuu
      901 gccccgaaug ugcucuacca guaccuuuuc cucuuuacuu gguaccuccu gaucgcggua
      961 uucuucacua accucaucag uuguuuccuc cacauuucug agauguucuu cucuaacggu
     1021 acguacaaca ggaugauaga ucaaggaaug uugccagaca agcccaguua ucgguacguc
     1081 uucaugaaca uuggcgccgg uggcagagag auaguccaga uucuaacaga caauuccaac
     1141 ccccucuugu uuagcaagau auuugacgau cuuaccaauu uacuaaucac uacuuccaaa
     1201 aacgcugacg ucauugaaaa ccugucgaag uuggauuccu ccguaauuga acuaggcagc
     1261 aaagacucaa ucuaa
//

Example 2

Input file 1: N-terminal_pep.gb

LOCUS       Mle-Panxα3                66 aa                     UNA 02-JAN-2015
DEFINITION  cDNA - ML036514a.
ACCESSION   Mle-Panxα3
VERSION     Mle-Panxα3
KEYWORDS    .
SOURCE
  ORGANISM  . . . . .
            .
FEATURES             Location/Qualifiers
     CDS             order(1..50,51..66)
                     /modified_by="User"
     N-term          1..28
     TMD1            29..49
     ECL1            50..66
ORIGIN
        1 mlllgslgti knlsifkdls lddwldqmnr tfmflllcfm gtivavsqyt gkniscdgft
       61 kfgedf

//
LOCUS       Mle-Panxα4                66 aa                     UNA 02-JAN-2015
DEFINITION  cDNA and genomic - ML129317a.
ACCESSION   Mle-Panxα4
VERSION     Mle-Panxα4
KEYWORDS    .
SOURCE
  ORGANISM  . . . . .
            .
FEATURES             Location/Qualifiers
     N-Term          1..27
     TMD1            28..48
     ECL1            49..66
ORIGIN
        1 mviellagyk glspfkdatv ddswdqinrc yvfiamvvmg avttmrqysg tliacdgftk
       61 fhpqfa
//

Input file 2: Mle-Panxα3.fa

>Mle-Panxα3 cDNA - ML036514a.
ATGTTGTTGCTCGGCTCACTCGGAACGATCAAGAACTTGAGCATCTTCAAAGACCTGTCC
TTGGACGACTGGCTGGATCAGATGAACAGGACCTTCATGTTTCTACTGCTCTGTTTCATG
GGAACAATTGTCGCCGTTAGTCAGTACACTGGTAAAAACATATCTTGCGATGGCTTTACG
AAGTTCGGAGAAGATTTCTCGCAAGACTACTGCTGGACCCAGGGCTTGTACACGATTAAA
GAAGCGTACGACTTGCCCGAGTCCCAGATCCCGTATCCTGGGATTATCCCTGAAAACGTG
CCGGCATGTAGAGAGCACGCTCTGAAAAACGGAGGAAAGATAGTCTGCCCTCCTGAAGAT
CAAGTGAAGCCCCTGACCCGGGCTCGACATCTCTGGTACCAGTGGATACCTTTCTACTTC
TGGGTGATAGCTCCAGTCTTCTATCTCCCTTACATGTTTGTGAAAAGGATGGGACTTGAC
AGAATGAAACCTCTGTTGAAGATCATGAGCGACTACTACCACTGCACTACAGAGACACCT
TCAGAGGAGATAATAGTGAAGTGTGCAGACTGGGTATACAACAGTATAGTAGACAGGCTG
TCAGAGGGCAGCAGCTGGACAAGCTGGAGAAACAGACACGGTCTTGGTCTGGCTGTCTTG
GTCAGCAAGTTCATGTATCTCGGAGGTAGTGTCCTCGTCATGATGATGACCACTCTCATG
TTCCAGGTTGGTGATTTCAAGACGTACGGTATAGAGTGGTTGAGGCAGTTCCCTAATCCA
GAAAACTATTCGACCTCAGTTAAACACAAACTATTCCCCAAAATGGTAGCCTGTGAGATA
AAACGATGGGGCACTACCGGGCTAGAAGAGGAGAATGGAATGTGTGTCCTTGCCCCGAAT
GTCATCTACCAGTACATTTTTCTAATCATGTGGTTCGCTCTAGCCATCACCATATGCACC
AACTTCGGCAACATATTTTTCTATCTCTTCAAGCTGACAGCCACTAGATACACTTACAAC
AAATTGGTGGCCACAGGACATTTCTCCCACAAGCACCCAGGTTGGAAGTTCATGTACTAC
CGGATTGGGACGTCAGGTCGCGTTCTCCTGAACATTGTCGCTCAAAACACGAACCCTATC
ATTTTCGGGGCTATCATGGAAAAACTGACACCTTCAGTCATTAAGCATTTGAGGATAGGT
CACGTGCCCGGGGAGTATTTAACGGACCCAGCATAG

Usage

$: sb Mle-Panxα3.fa N-terminal_pep.gb -fp2n

Output

Warning: Mle-Panxα4 is in the protein file, but not in the cDNA file

LOCUS       Mle-Panxα3              1236 bp    DNA              UNK 01-JAN-1980
DEFINITION  Mle-Panxα3 cDNA - ML036514a.
ACCESSION   Mle-Panxα3
VERSION     Mle-Panxα3
KEYWORDS    .
SOURCE      .
  ORGANISM  .
            .
FEATURES             Location/Qualifiers
     CDS             order(1..198,1..198)
                     /label="ML036514a"
     N-term          1..84
     TMD1            85..147
     ECL1            148..198
ORIGIN
        1 atgttgttgc tcggctcact cggaacgatc aagaacttga gcatcttcaa agacctgtcc
       61 ttggacgact ggctggatca gatgaacagg accttcatgt ttctactgct ctgtttcatg
      121 ggaacaattg tcgccgttag tcagtacact ggtaaaaaca tatcttgcga tggctttacg
      181 aagttcggag aagatttctc gcaagactac tgctggaccc agggcttgta cacgattaaa
      241 gaagcgtacg acttgcccga gtcccagatc ccgtatcctg ggattatccc tgaaaacgtg
      301 ccggcatgta gagagcacgc tctgaaaaac ggaggaaaga tagtctgccc tcctgaagat
      361 caagtgaagc ccctgacccg ggctcgacat ctctggtacc agtggatacc tttctacttc
      421 tgggtgatag ctccagtctt ctatctccct tacatgtttg tgaaaaggat gggacttgac
      481 agaatgaaac ctctgttgaa gatcatgagc gactactacc actgcactac agagacacct
      541 tcagaggaga taatagtgaa gtgtgcagac tgggtataca acagtatagt agacaggctg
      601 tcagagggca gcagctggac aagctggaga aacagacacg gtcttggtct ggctgtcttg
      661 gtcagcaagt tcatgtatct cggaggtagt gtcctcgtca tgatgatgac cactctcatg
      721 ttccaggttg gtgatttcaa gacgtacggt atagagtggt tgaggcagtt ccctaatcca
      781 gaaaactatt cgacctcagt taaacacaaa ctattcccca aaatggtagc ctgtgagata
      841 aaacgatggg gcactaccgg gctagaagag gagaatggaa tgtgtgtcct tgccccgaat
      901 gtcatctacc agtacatttt tctaatcatg tggttcgctc tagccatcac catatgcacc
      961 aacttcggca acatattttt ctatctcttc aagctgacag ccactagata cacttacaac
     1021 aaattggtgg ccacaggaca tttctcccac aagcacccag gttggaagtt catgtactac
     1081 cggattggga cgtcaggtcg cgttctcctg aacattgtcg ctcaaaacac gaaccctatc
     1141 attttcgggg ctatcatgga aaaactgaca ccttcagtca ttaagcattt gaggataggt
     1201 cacgtgcccg gggagtattt aacggaccca gcatag
//