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You may try the data for "Colon Adenocarcinoma" made by the TCGA project: http://gdac.broadinstitute.org/runs/analyses__2015_04_02/reports/cancer/COAD/ The file with mutations called by the tumor against a matched normal, http://gdac.broadinstitute.org/runs/analyses__2015_04_02/reports/cancer/COAD/MutSigNozzleReport2.0/COAD-TP.final_analysis_set.maf What ...


The locations of a gene on a bacterial chromosome is determined arbitrarily, so you would not expect coding sequences to necessarily have the same numerical values. Remember that the bacteria's transcription machinery will use promoters in the genetic sequence to determine where to start transcription, so the actual start location doesn't really matter -- ...


The error rate of PCR is still very high in comparison to natural bacteria DNA replication of its plasmids. Natural bacteria DNA replication has an error rate of approximately 1 in 10 billion, and the best PCR polymerase commercially available (Q5 from NEB) has an error rate of approximately 1 in 1 million. Therefore, cloning fragments into bacteria and ...


You can use PCR products in Sanger sequencing; it is very common. Using PCR products instead of cloned genes does raise a set of problems that are less of a concern than with cloned sequences, such as the presence of incomplete or incorrect PCR products, but there are standard and simple solutions for most of these concerns.


I wouldn't necessarily expect regions of heterozygosity to be apparent from a consensus fasta. I'd eyeball if you know some potential sites, or run your .bam through something that will call SNPs.


If you are looking for simple one off queries it might be better to load the BAM file and a relevant reference genome into a browser like IGV and simply navigate to that specific position. For some data I had lying around a heterozygous SNP would look like the picture below, there has been an A to G SNP and a C to T: For longer lists of queries I would ...


As a starting point I would suggest you look at genomes of thermophiles and hyperthermophiles (organisms that thrive at upwards of 40 °C and 60 °C respectively), which are often found near underwater volcanos or hot springs. For instance, one could do a genomic analysis of the archaean Methanocaldococcus jannaschii, comparing it to mesophilic species of ...

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