I just have do an multiple sequence alignment (about 15000 sequences) between different strains of a bacteria for determine its conserved regions, but near of 1% of sequences have 80 or 85% of identity and it generate problems for the determination of conserved regions, that sequences could be the same gene or could be a wrong of the sequencing uploaded to the database?
Are you sure you have DNA of a single species in such samples? In the past, I had a similar problem for 16S rRNA and I realized some of my sample looked like pure cultures but were coculture bacteria. In my case my sample was not pure, so to say. In a case like mine, you can check that in the graphs you obtain from sequencing your gene fragment and you would see mixed graph peaks for the nucleotides.
Hi Juan Carlos Cambronero-Heinrichs! The aligned sequences corresponds to the AdeB gene for A. baumannii downloaded from a database. In the case of the variable sequences, I have searched it in BLAST and I have found that all the sequences shows 100% of identity for adeJ gene, this gene codifies AdeJ protein, a homologue protein to AdeB. This likely could be related to the fact that when that genomes were sequenced, adeJ wasn't discovered yet and in the annotation process, adeJ was named adeB because that gene is similar to adeJ. Fortunately, there are more than 1 genomes sequenced for the same strain and in ones the gene is named adeB and for others in the same position, the gene was named adeJ.
- Badges
- Science method