bioinformatics

问题 I have two data.frames each with three columns: chrom, start & stop, let's call them rangesA and rangesB. For each row of rangesA, I'm looking to find which (if any) row in rangesB fully contains the rangesA row - by which I mean rangesAChrom == rangesBChrom, rangesAStart >= rangesBStart and rangesAStop <= rangesBStop . Right now I'm doing the following, which I just don't like very much. Note that I'm looping over the rows of rangesA for other reasons, but none of those reasons are likely to

问题 I am working with NCBI Reference Sequence accession numbers like variable a : a <- c("NM_020506.1","NM_020519.1","NM_001030297.2","NM_010281.2","NM_011419.3", "NM_053155.2") To get information from the biomart package I need to remove the .1 , .2 etc. after the accession numbers. I normally do this with this code: b <- sub("..*", "", a) # [1] "" "" "" "" "" "" But as you can see, this isn't the correct way for this variable. Can anyone help me with this? 回答1: You just need to escape the

问题 I am trying to install FSL on Ubuntu 16.04 64-bit. I followed procedure at neurodebian website, selected the correct package, specified ALL software. When I copy-paste the commands in my terminal the pipe hangs without prompting for my sudo password: wget -O- http://neuro.debian.net/lists/xenial.de-m.full | sudo tee /etc/apt/sources.list.d/neurodebian.sources.list I also tried to separate the pipe in the two commands. The first one runs, the second asks for my password and then hangs. I con't

问题 In bioinformatics/microbial ecology literature a fairly common practice is to concatenate multiple sequence alignments of multiple genes prior to building phylogenetic trees. In R terminology it may be clearer to say 'merge' these sequences by the organism they came from, but I'm sure examples are better. Say these are two multiple sequence alignments. library(Biostrings) set1<-AAStringSet(c("IVR", "RDG", "LKS")) names(set1)<-paste("org", 1:3, sep="_") set2<-AAStringSet(c("VRT", "RKG", "AST")

问题 I want to store DNA sequences of size n in the described data structure. Each hash could contain the keys C,G,A,T who will have hash values. These hash values will be the exact same kind of hashes - they will have four keys, C,G,A,T who will have hash values. This structure is consistent for n levels of hashes. However, the last level of hashes will instead have integer values, which represent the count of the sequence from level 1 to level n. Given the data ('CG', 'CA', 'TT', 'CG'),

问题 I am using a new bioinformatics tool called Giggle and I have installed the python wrapper on my system. Even though the scenario is quite specific, I think the problem is quite general. This function: index = Giggle.create("index", "HMEC_hg19_BroadHMM_ALL.bed") should create an index based on several (or in this case one) .bed file. The bed files look like this: chr1 10000 10600 15_Repetitive/CNV 0 . 10000 10600 245,245,245 chr1 10600 11137 13_Heterochrom/lo 0 . 10600 11137 245,245,245 chr1

问题 I have a large data set and I want to write a custom merge function to use with apply but I can't solve a certain issue. I can't use a loop as it will take too long. The data roughly looks like this; # [ Name, Strand, Start, End ] R1 = c( 'GeneA', '+', 1000, 1500 ) R2 = c( 'GeneA', '+', 1510, 2000 ) R3 = c( 'GeneA', '+', 2001, 2500 ) R4 = c( 'GeneB', '-', 3100, 4000 ) The data is a data.frame with rows R1:R4 So far I can get a function which compares Ri and Rj (j = i +1) and merges them if

问题 I would like to subset some of its columns according to another data frame's rows. So the two data frames are as shown below: df1 <- structure(list(ID = structure(c(3L, 1L, 2L, 5L, 4L), .Label = c("cg08", "cg09", "cg29", "cg36", "cg65"), class = "factor"), chr = c(16L, 3L, 3L, 1L, 8L), gene = c(534L, 376L, 171L, 911L, 422L), GS12 = c(0.15, 0.87, 0.6, 0.1, 0.72), GS32 = c(0.44, 0.93, 0.92, 0.07, 0.91), GS56 = c(0.46, 0.92, 0.62, 0.06, 0.87), GS87 = c(0.79, 0.93, 0.86, 0.08, 0.88)), .Names = c(

问题 I have a fasta file which contains protein sequences. I'd like to select sequences with more than 300 amino acids and Cysteine (C) amino acid appears more than 4 times. I've used this command to select sequences with more than 300 aa: cat 72hDOWN-fasta.fasta | bioawk -c fastx 'length($seq) > 300{ print ">"$name; print $seq }' Some sequence example: >jgi|Triasp1|216614|CE216613_3477 MPSLYLTSALGLLSLLPAAQAGWNPNSKDNIVVYWGQDAGSIGQNRLSYYCENAPDVDVI

问题 I just start working with perl and I have a question. I have PHYLIP file and I need convert it into FASTA. I start writing a script. Firstly, i removed scpaces in lines, now i need to align all lines that in every line should be 60 aminoacids and sequances identificator should be printed in new line. Maybe someone could give me some advice? 回答1: BioPerl Bio::AlignIO module might help. It support the PHYLIP sequence format : phylip2fasta.pl use strict; use warnings; use Bio::AlignIO; # http:/