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In general you should use a base calling algorithm to generate the sequences from the chromatogram and not directly convert it to fasta (Courtesy: Sven [SEQanswers] ). As mentioned in the link, phred and TraceTuner are popular base calling software that can generate a fasta output. The software mentioned by The Nightman can be used for converting .ab1 to ...


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First of all, the reference genome strand specificity is referred to as sense (positive strand) or antisense (negative strand). Here's a somewhat incorrect note from the wiki article under sense (molecular biology) The strand names actually depend on which direction you are writing the sequence that contains the information for proteins (the "sense" ...


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It depends on what type of data you have, really. There are methods developed solely for quantifying relative expression based on count data, such as using edgeR or limma-voom. You don't need to correct for gene length to estimate fold-changes of relative expression, what you need to do is normalise by library size first (and in the process obtain log2 ...


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This will be a complete answer, but it's got code, so it won't work as a comment. Working backwards from rtree(3), here's a way to build a phylo object from component parts, which might be helpful: children <- c(5, 1, 2, 3) parents <- c(4, 5, 5, 4) x <- matrix(c(parents, children), ncol = 2) tr <- list(edge = x, tip.label = 1:3, Nnode = 2) ...


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Another good alternative is Swiss-PDB viewer. It is free, small, easy to install/use and is available for different OS (I had used it in Windows XP with 256MB RAM! Some features don't work well with low RAM but nonetheless it is not very resource hungry). It is good for the kind of tasks you are interested in. But it is not online (Actually I fail to ...


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This is an answer simply because I can't fit it all in a comment, or several... To install and run PyMOL, you'll need a few extras. They are all free and open-source: Python 2.7.10: Make sure you choose to install pip during the setup process, and also choose to add Python to your PATH, if that option is given. Also, note whether you installed the 32-bit ...


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If there is a such a site, I have never encountered it. Since you say you have the genomic coordinates for each primer it seems to me like all you need is a list of the genomic coordinates of every transcribed exon in the human genome. Assuming that is correct then you are in luck because such lists do exist in the form of a GFF3 file. You should be able to ...


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Typical possibilities that come to mind are programs available in EMBOSS and Staden. However the question of how to access the sequence data stored in .ab1 files has been asked on Biostars a number of times, so I suggest having a look at the various answers there for options that are suitable for your environment and use case, see Biostars search "ab1".


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DNA Baser has a batch abi to fasta converter here. After files have been converted to .fa files, they can be concatenated together in UNIX/MAC using cat *fa > output.fa


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From what I understood of your code and what you are asking I am guessing that you do the following: Generating a virtual set of 40 individuals (lines) of which you have 200 measurements (repetitions). You say that they are full siblings, so they share both parents. Then you use the lmer function (which I am not familiar with) to give you the total ...



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