Interspecies comparison of 25 kb gene
Hello Friends
I sequenced a gene in human, cynomongus and dog. Now I would like to alingn the three genes and if possible align them to
homologue genes of even further related species. I mainly need to find differences in the Codons. This has shown to be hard because some the coding strang of the gene is not always the same compared to other species (+ or - strang) and the lenght of the introns differ quite a lot. Compared aminoacid sequences show quite some similarity. Can anyone help me with a tutorial or any suggestions which program to use?
Im quite a newbie at genetics and would be very thankful.
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"Sequenced" as in still individual reads (sanger/NGS?) need to be assembled/aligned or "finished" (single sequence files with sequence ~25kb) ready for translation into protein/comparison?
Hello pedee87!
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Reopened, there are some uncovered details here, sorry for that.
The nucleotide level comparison would be mostly meaningless, stay on the protein level and do a standard MSA. In addition you can plot the intron-exon structure for each gene. If you want to compare codon usage, you should look at the coding sequence (CDS) only. Try to extract the CDS of your gene from a genome browser, Ensembl, UCSC.