The problem I am facing is that I am getting errors like Warning: Sequence 280 "DNEG10010009 " does not begin with a recognised start codon. Warning: Sequence 280 "DNEG10010009 " has 16 internal stop codon(s)
The input I have provided is a sequence of Nucleotide sequences for each individual gene of Bacillus Subtilis 168.
My question is how do I solve this error? Actually all I really want to do is to calculate various values like codon adaptation index,codon bias index,number of optimal codons and so on for each gene of Bacillus Subtilis 168 .For that I am using the software CODONW.I would also like to know if the sequence that I am providing as input is correct or not and if not what should I provide as input.
The other doubt I have is that do I input Open Reading Frames for Codon Analysis.If a particular gene sequence has multiple ORF's which one should be chosen?
Here are some sequences for which I am getting an error: Please tell me how to solve this error.I think I need to convert them to ORF's before giving them as input but I am not sure.The errors I am getting are only for NonEssential genes of Bacillus Subtilis 168.
>DNEG10010082 TTGATAGGGCAGAAAGCTTGGGTGAACATTGGCAAGACCGAATTCATCTTGCTTCTTGTC GTTGGAATTTTAACCATCATCAATGTACTAACAGCAGACGGAGAAAAGCGTACATTTCAT TCTCCTAAGAAAAAGAATATCAATCATTTAACCCTTTATGATTGCGTATCTCCGGAAGTT CAGAACAGTATAAACGAAACAGGGCGTGTGACAAACTTCTTTTGA >DNEG10010083 ATGAATCAAAATCAGTTGATATCGGTAGAGGATATCGTATTTCGATATCGGAAGGACGCA GAAAGACGAGCACTAGACGGCGTCTCCCTGCAGGTGTATGAGGGTGAATGGCTTGCAATC GTAGGTCATAACGGTTCAGGGAAATCAACACTGGCCCGGGCATTGAATGGTTTAATTCTT CCTGAATCAGGCGACATTGAGGTTGCCGGGATTCAATTGACAGAGGAATCTGTTTGGGAA GTGCGTAAGAAGATAGGTATGGTCTTTCAAAATCCGGATAACCAATTTGTCGGAACGACT GTTCGCGATGATGTGGCTTTTGGTTTAGAAAACAATGGTGTACCGCGGGAAGAAATGATT GAGAGAGTAGACTGGGCAGTAAAACAGGTGAATATGCAAGATTTTCTCGATCAAGAGCCG CACCATCTCTCCGGAGGCCAAAAGCAGAGAGTTGCGATTGCGGGGGTTATTGCCGCACGT CCTGATATTATTATCTTAGATGAAGCAACATCCATGCTTGATCCGATCGGGCGAGAAGAA GTGCTTGAAACGGTAAGACATTTAAAAGAGCAGGGCATGGCGACTGTCATATCCATTACA CATGACCTGAATGAGGCAGCAAAAGCAGACAGGATCATTGTCATGAATGGCGGTAAAAAA TATGCTGAAGGGCCGCCTGAAGAGATTTTTAAATTGAATAAAGAACTTGTTCGAATTGGG CTTGATTTACCCTTCTCATTCCAGCTTAGCCAGCTTTTAAGAGAAAATGGACTGGCTTTG GAAGAAAACCATTTGACTCAGGAAGGGCTGGTGAAAGAGCTGTGGACATTACAATCAAAG ATGTAG