I need to identify the sequence of a gene in the complete genome sequence . I thought it was simple, instead it is not a straightforward task !
My method was the following: I downloaded the FASTA format file of the complete genome sequence of the archaea organism that I am studying, that is CP003685, and then I downloaded the CDS file from NCBI by clicking on ">Send to>Coding Sequencing>FASTA Nucleotide>Create File". In this way I have a txt file (always FASTA format file) in which I find a sequence for each gene (if I am not wrong).
So for example, I should find, in the complete genome sequence, the sequences of the CDS file (the last that I downloaded), right?
For example, if I consider:
>lcl|CP003685.1_cds_AFN03983.1_1007 [locus_tag=PFC_05180] [protein=DNA protection protein DPS] [protein_id=AFN03983.1] [location=complement(940023..940580)] [gbkey=CDS] ATGCCAGAGCATAATAGGAGATTAGTTGAAAGGACAGGAATAGATGTAGAGAAGCTGTTGGAACTTCTCA TTAAAGCGGCTGCAGCAGAGTTCACAACGTATTATTACTACACTATACTTAGAAACCATGCAACAGGTCT GGAAGGAGAAGCAATTAAGGAGATTATCGAAGATGCTAGACTTGAGGACAGAAACCATTTTGAAGCCCTC GTGCCAAGAATATACGAGCTTGGAGGAGAATTACCAAGGGATATTCGGGAATTTGCAGATCTAGCTTCTT GTAGAGATGCCTACCTACCAGAAGAGCCCACTATAGAGAACATTCTAAAAGTCCTACTCGAAGCTGAGAG ATGTGCAGTTGGAGTCTATACAGAAATATGCAACTACACTTTTGGAAAGGATCCAAGGACTTATGATTTG GCCCTTGCCATATTACATGAAGAGATAGAGCATGAAGCATGGTTTGAAGAGCTCTTGACTGGAAAGCCGA GTGGTCACTTTAGAAGAGGAAAGCCTGGGGAAAGTCCATATGTCTCAAAGTTTTTGAAAACTAGATAG
I should find in the complete genome sequence, this sequence, right ? But this is not. Why?
I suspect that I miss very important passages.
Thank you in advance.