diff --git a/README.md b/README.md index 78c2bfdae9e5c79d0b794ca3cc7f33e3b611fcf3..fd1ca6b1580d75c5432b7765b62b26f4abf62b87 100644 --- a/README.md +++ b/README.md @@ -99,7 +99,7 @@ VQGWSLCALLYGLIGTCRLNGIDPEAYLRHILSVLPEWPSNRVGELLPWNVVLTNK ```bash eFASTA -f Ecoli.O104H4.plsm.fna -c CP003291:31400-31293 -orf -stop ``` -This command line allows writing the two files _seq.fna_ and _seq.faa_ containing the ORF and its translation, respectively, with the two ending-up codons stop: +This command line allows writing the two files _seq.fna_ and _seq.faa_ containing the ORF and its translation, respectively, with the two ending-up stop codons: ``` >CP003291.1 plasmid pAA-EA11::31436-31263 TGAGTACAGGGCTGGAGCTTGTGTGCACTGCTGTACGGGCTGATCGGCACCTGCCGTCTGAACGGTATCGATCCGGAAGCGTATCTGCGCCATATTCTGAGCGTACTGCCGGAATGGCCTTCCAACCGAGTTGGCGAACTCCTGCCATGGAACGTAGTACTCACCAATAAATAA @@ -128,7 +128,7 @@ VQGWSLCALLYGLIGTCRLNGIDPEAYLRHILSVLPEWPSNRVGELLPWNVVLTNK ```bash eFASTA -f Ecoli.O104H4.plsm.fna -c CP003291:31400-31293 -fcds -start PROK ``` -This command line allows writing the two files _seq.fna_ and _seq.faa_ containing the CDS and its translation, respectively, by considering each of the three codons ATG, GTG and TTG as a putative codon start: +This command line allows writing the two files _seq.fna_ and _seq.faa_ containing the CDS and its translation, respectively, by considering each of the three codons ATG, GTG and TTG as a putative start codon: ``` >CP003291.1 plasmid pAA-EA11::31418-31266 TTGTGTGCACTGCTGTACGGGCTGATCGGCACCTGCCGTCTGAACGGTATCGATCCGGAAGCGTATCTGCGCCATATTCTGAGCGTACTGCCGGAATGGCCTTCCAACCGAGTTGGCGAACTCCTGCCATGGAACGTAGTACTCACCAATAAA @@ -138,11 +138,11 @@ TTGTGTGCACTGCTGTACGGGCTGATCGGCACCTGCCGTCTGAACGGTATCGATCCGGAAGCGTATCTGCGCCATATTCT MCALLYGLIGTCRLNGIDPEAYLRHILSVLPEWPSNRVGELLPWNVVLTNK ``` -##### Coding Sequence (CDS) with alternate codon start and codon stop +##### Coding Sequence (CDS) with alternate start codon and stop codon ```bash eFASTA -f Ecoli.O104H4.plsm.fna -c CP003291:31400-31293 -fcds -start PROK -stop ``` -This command line allows writing the two files _seq.fna_ and _seq.faa_ containing the CDS and its translation, respectively, by considering each of the three codons ATG, GTG and TTG as a putative codon start, and including the termination codon: +This command line allows writing the two files _seq.fna_ and _seq.faa_ containing the CDS and its translation, respectively, by considering each of the three codons ATG, GTG and TTG as a putative start codon, and including the termination codon: ``` >CP003291.1 plasmid pAA-EA11::31418-31263 TTGTGTGCACTGCTGTACGGGCTGATCGGCACCTGCCGTCTGAACGGTATCGATCCGGAAGCGTATCTGCGCCATATTCTGAGCGTACTGCCGGAATGGCCTTCCAACCGAGTTGGCGAACTCCTGCCATGGAACGTAGTACTCACCAATAAATAA