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Commit 9aec40c0 authored by Alexis  CRISCUOLO's avatar Alexis CRISCUOLO
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Update README.md

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......@@ -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
......
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