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2

@kmm's code works with a few tweaks. One problem your edgelist has is that it contains a singleton node, which ape does not like to deal with. Turning it into a proper phylo object means removing the singleton 'root' node and instead making the child of this singleton node the root. Here is an example using a slightly larger tree, which demonstrates how to ...


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You should first understand what the meaning of E-value is. E-value is the likelihood of a random match having a certain score in given database. So, you are right that a database is required to calculate E-value. The online algorithm calculates it from not necessarily the nr database but any selected target database which could be RefSeq or organism ...


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You do not need the nr database for BLAST to calculate an E-value. It will be calculated based on the alignment of n sequences. The exact procedure is mathematically complex but if you want to read the original paper it is here: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC53667/pdf/pnas01031-0226.pdf a simplified version you will find here: ...


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Well, Mitochondrial DNA CAN be linear (in some organism), see the wikipedia page on this In most multicellular organisms, the mtDNA - or mitogenome - is organized as a circular, covalently closed, double-stranded DNA. But in many unicellular (e.g. the ciliate Tetrahymena or the green alga Chlamydomonas reinhardtii) and in rare cases also in ...


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Q1: Yes, the CIGAR string operation 'M' means you can have both matches and mismatches. For example if you have a CIGAR string 10M, then you could have 10 bases that matched perfectly or you could have 5 matches and 5 mismatches. In this case, you have what are known as SNPs (or single nucleotide polymorphisms). Q2: In your case, you have 99 matches, 170661 ...


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In addition to the 4 nucleotide letters, there are letters that mean "the letter is one of these two or three: M = aMine = A or C R = puRine = A or G W = Weak (two hydrogen bonds) = A or T S = Strong (three hydrogen bonds) C or G Y = pYrimadine = C or T K = Ketone = G or T B = not A D = not C H = not G U = not T I would guess the the lowercase ...


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You can use Ensembl (http://www.ensembl.org/index.html) to retrieve orthologues of the protein, and align them using one of many free, web based programs (such as ClusterOmega)


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You can start off by studying how an miRNA regulates the functioning of a gene. it basically binds to the 3'UTR and 5'UTR of an mRNA and restricts its translation. There will be genes associated with the disease of your interest, find out the miRNA's related to those genes. You can use micro array data to find out the up-regulated genes. Target scan human, ...


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BWA-mem (like most aligners), takes a normal single-stranded fasta file (I've never seen one with both strands listed) and aligns to both strand.


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Theoretical ecology From wikipedia Theoretical ecology is the scientific discipline devoted to the study of ecological systems using theoretical methods such as simple conceptual models, mathematical models, computational simulations, and advanced data analysis. Effective models improve understanding of the natural world by revealing how the dynamics of ...


2

Allele frequency is simply the frequency at which a specific allele is found in members of a population. Let's take the following example from the site you referenced: The first column merely has the name of the allele, A*01. The second column is the population from which individuals were genotyped. Skipping ahead, the fifth column is the number of people ...


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Can you provide the gene of interest? You can usually search Entrez for the gene symbol in the dbSNP database, which will pull up a NCBI Entrez page for SNPs located in the gene and will also give an indication of their clinical significance (benign or otherwise). Alternatively, if you have a specific disease in mind, you can check more specific ...


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Just rename the file to .pdb - in other words, .ent files are PDB format: The archival PDB files will be distributed with the reserved conventional names, in the form pdbentry_id.ent, where entry_id is a PDB 4-letter code, e.g. pdb1abc.ent, for PDB format entries; rentry_idsf.ent, e.g. r1abcsf.ent, for X-ray experimental data; entry_id.mr, e.g. 1abc.mr, ...


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You might be confused about what "heuristic" means. "Heuristic" doesn't mean random or arbitrary, instead, an algorithm is termed "heuristic" if it employs a shortcut which means that it does not necessarily yield the theoretically best result. For BLAST, this shortcut is the assumption of first matching the fixed-length words prior to extending the match. ...


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Here are a few metrics you can calculate to get you started. You can use R to perform these calculations. Net Diversification Rate (r) Net diversification rate is (rate of speciation - rate of extinction). You can calculate it using the bd.ms or bd.km functions in the geiger package for R. r = 1: r = 2: Tree Imbalance: Colless index (I) Colless's ...


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The link that ddiez has mentioned, has a download link for a zip file (fidist2). The zip file contains windows executables and C-codes. Just compile the C-codes in your terminal. This is from the readme: The .exe files are pc binaries, which is only what most people want. I include the source file in case anyone wants to play with them. In this case ...


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As mentioned by @WYSIWYG in his answer the quality scores in FASTQ file format are encoded in ASCII characters, and there has been several ways to encode this information. The wikipedia FASTQ page that you link in your question describes some (not sure if all) the different alternatives. Now, why do we have this wide range of characters for the quality ...



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