Try import MySQLdb db = MySQLdb.connect(host=”localhost”, user=”user”, passwd=”password”, db=”database”) cur = db.cursor() cur.execute(“SELECT common_name , genus , species FROM table WHERE sequence LIKE ‘MDPSSID%'”) 1 solved Searching through database with python
To get started with, FASTA is text file format. To write text files check MATLAB documentation of fopen, fprintf and fclose. To load the text from the data files you’ve written you can use fopen, fscanf and fclose. Actually, MATLAB…
These are the steps I would take: 1) align the sequences 2) read each column of the alignment and produce a list of the different possible amino acids in each position 3) each position can now be represented by a…
Many options here. Unfortunately you don’t show any effort to resolve the problem or even to make it clear and reproducible. For example, using ifelse : dat <- read.table(text=””aaa” 28 “aac” 8 “aag” 20″) dat$V1 <- with(dat,ifelse(V1 %in% c(‘aaa’,’aag’),’K’,’N’)) dat…
I suppose you have a sequence of nucleotides from DNA and you want to know if there is any gen there in any of the three frames of the sequence. I recommend to use Biopython to do it but there…
create the spans with javascript and style the spans with css: Javascript $(‘document’).ready(function() { $(‘.protein’).each(function() { var target = $(this).html(); target = target.split(“”); var result = “”; for (var i = 0, len = target.length; i < len; i++)…
I think something like this should do what you want. We use a hash to gather the ‘reference’ file and turn it into a set of keys with an empty array. Then we iterate on the other files, extracting ‘3…
Item 1: I’m not versed in k-mer counting and the definition of x is a bit shaky. If you could update your question, then I’ll try to address point 1. But, to me it seems as if you just need…
We may use either of the following: do.call(function (…) paste(…, sep = “-“), rld[groups]) do.call(paste, c(rld[groups], sep = “-“)) We can consider a small, reproducible example: rld <- mtcars[1:5, ] groups <- names(mtcars)[c(1,3,5,6,8)] do.call(paste, c(rld[groups], sep = “-“)) #[1] “21-160-3.9-2.62-0″…
The d-neighborhood of the k-mer Pattern is the collection of all k-mers that are at most Hamming distance d from Pattern solved The d-neighborhood of the k-mer Pattern is the collection of all k-mers that are at most Hamming distance…
Why not learn the numerical representations for each base? This is a common problem in Neural Machine Translation, where we seek to encode “words” with a meaning as (naively) numbers. The core idea is that different words should not be…
Not completely clear on what you want; maybe this: my $seq; my %idSeq; while ( my $line = <$INPUT> ) { if ( my ($name) = $line =~ /^>(.*)/ ) { $idSeq{$name} = length $seq || 0; } else {…