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mariodosreis / tai

The tRNA adaptation index
GNU General Public License v2.0
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64 anticodon order in file "ecolik12.trna" #3

Closed lw157 closed 3 years ago

lw157 commented 3 years ago

Hi Mario, Thanks for developing this tool. I am confused with file "ecolik12.trna", which has 64 values. While "ecolik12.m" has only 61 values for each ORF/gene, and their codon order is in the "QUICK TUTORIAL". As you describe in the README, "ecolik12.trna" include the STOP codons. So, what are the exact order for those 64 codon? Thanks a lot.

Best, Liuyang

mariodosreis commented 3 years ago

This is not a software issue so it's being closed.

Codons are in TCGA ordering. Position of stop codons can be worked out from this (this is the standard codon ordering). README.md file has been updated to clarify this.

lw157 commented 3 years ago

Thank you so much, Mario. That is very helpful. I attached the order here based on your information. 1 TTT 2 TTC 3 TTA 4 TTG 5 TCT 6 TCC 7 TCA 8 TCG 9 TAT 10 TAC 11 TAA 12 TAG 13 TGT 14 TGC 15 TGA 16 TGG 17 CTT 18 CTC 19 CTA 20 CTG 21 CCT 22 CCC 23 CCA 24 CCG 25 CAT 26 CAC 27 CAA 28 CAG 29 CGT 30 CGC 31 CGA 32 CGG 33 ATT 34 ATC 35 ATA 36 ATG 37 ACT 38 ACC 39 ACA 40 ACG 41 AAT 42 AAC 43 AAA 44 AAG 45 AGT 46 AGC 47 AGA 48 AGG 49 GTT 50 GTC 51 GTA 52 GTG 53 GCT 54 GCC 55 GCA 56 GCG 57 GAT 58 GAC 59 GAA 60 GAG 61 GGT 62 GGC 63 GGA 64 GGG