<< btd_seqrcomplement BTD Amino Acids >>

BTD >> BTD > btd_seqshoworfs

btd_seqshoworfs

Open Reading Frames found in a nucleotide sequence

Calling Function

y = btd_seqshoworfs(x)

Arguments

y

String of single-letter codes specifying a nucleotide sequence

x

All open reading frames using the standard or an alternative genetic code (column of text: one frame per row).

Examples

nuSeq = 'TTTTTATTCTTTCTGCCAGGTACATCAGATCCATCAGGTCCGAGCTGTGTTGA'+..
        'CTACCACTGCTTTTCCCTTCGTCTCAGTTATGTCTTGGAAGAAGGCTTT'+..
        'GCGGATCCCCGGAGACCTTCGGGTAGCAACTGTCACCTTGATGCTGGCGATGCTGAGC';
y = btd_seqshoworfs(nuSeq)
// To get only the frames:
stripblanks(part(y,15:$))
--> y= btd_seqshoworfs(nuSeq)
 y  = 
!Frame 1 :       FLFFLPGTSDPSGPSCVDYHCFSLRLSYVLEEGFADPRRPSGSNCHLDAGDAE   !
!Frame 2 :       FYSFCQVHQIHQVRAVLTTTAFPFVSV*SWKKALRIPGDLRVATVTL*LA*LS   !
!Frame 3 :       FILSARYIRSIRSELC_LPLLFPSSQLCLGRRLCGSPETFG_QLSP_CWRC_    !
!Frame 4 :       RVVAVVVPLST*GFQRPLGVSEEGSVLTLLPFSSPSVVSSLDYLDY*DRLSYF   !
!Frame 5 :       ES_RS_FHCQRWASRGP_AFRKKVLY_LCFPFRHHQLCRAWTT_TTWTVFLIF   !
!Frame 6 :       SRSGRSSTVNDGLPEAPRRFGRRFCIDSASLFVTISCVEPGLPRLHGPSFLF    !

--> // To get only the frames:
--> stripblanks(part(y,15:$))
 ans  =
!FLFFLPGTSDPSGPSCVDYHCFSLRLSYVLEEGFADPRRPSGSNCHLDAGDAE  !
!FYSFCQVHQIHQVRAVLTTTAFPFVSV*SWKKALRIPGDLRVATVTL*LA*LS  !
!FILSARYIRSIRSELC_LPLLFPSSQLCLGRRLCGSPETFG_QLSP_CWRC_   !
!RVVAVVVPLST*GFQRPLGVSEEGSVLTLLPFSSPSVVSSLDYLDY*DRLSYF  !
!ES_RS_FHCQRWASRGP_AFRKKVLY_LCFPFRHHQLCRAWTT_TTWTVFLIF  !
!SRSGRSSTVNDGLPEAPRRFGRRFCIDSASLFVTISCVEPGLPRLHGPSFLF   !

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