Results for "R"
Top-level pages
Ancestral sequence reconstruction steps !
Ancestral sequence reconstruction (ASR) – also known as ancestral gene/sequence reconstructio...sp;protein. The idea of protein 'resurrection' was sugge...ent of algorithms and of better sequencing and synthesis tech...c signal, is possible to perform with Tree-Puzzle "http://www...2173 days ago
Gap filling or Contigs extensions tools !
There are many tools to perform gap filling using Illumina short reads, for example "GapFiller: a de novo assembly approach to fill the gap within pa...//genomebiology.com/2010/11/4/R41 Also SOAPdenovo has ha...ssembly C' from C and the new reads identified in (a) and (b)...2159 days ago
LINKS scaffolder bloomfilter setting !
➜ bin git:(master) ✗ ls -l total 68 drwxrwxr-x 3 urbe urbe 4096 Jun 15 12:15 lib -rwxrwxrwx 1 urbe urbe 65141 Jun...ter.so -O3 ➜ swig git:(master) ✗ cd .. ➜ bloomfilter git:...minimum number of links (k-mer pairs) to compute scaffold (d...2145 days ago
Understanding BLASTn output format 6 !
BLASTn output format 6 BLASTn maps DNA against DNA, for example gene sequences against a reference genomeblastn -query ...xpect value 12. bitscore bit score Define...ceevalue Expect valuebitscore Bit scorescore Raw scor...2132 days ago
Interview Puzzles for Bioinformatician !
These are some of the most famous Interview Puzzles being asked in top tech companies.Here is a list of Top 25 puzzles...ve been asked in top Tech Interview. 2 Eggs and 100 Floor...itches Find the minimum number of aircraft Burning ropes to...2113 days ago
My commonly used commands in Bioinformatics
...I, I've found it useful to use MUMmer to extract the specific changes that...minimap -t 24 assembly.fasta long_reads.fastq.gz | racon -t 24 lo...ly.fasta racon_assembly.fasta nucmer -p nucmer assembly.fasta raco...MUMmer -> SNP table) solves the problem I originally raised in t...2104 days ago
List of non-commercial NGS genotype-calling software
...aningful analysis of next-generation sequencing (NGS) data, which are produced extensively by genetics and genomics studies, relies crucially on the accurat...(bcftools) GATK http://www.broadinstitute.org/gsa/wiki/inde...rmation (NLDA) and a method for incorporating LD information...2090 days ago
Parallel Processing with Perl !
Here is a small tutorial on how to make best use of multiple processors for bioinformatics an...; push (@childs,$fork); }elseif($fork==0){you..._processors=8;my $fork= new Parallel::ForkManager($max_proces...iece of $file;######### end fork ###############$super_fork-&...2073 days ago
- The benchmark module is a great tool to know the time the code takes to run. The output is usually in terms of CPU time. This module provides us with a way to optimi...about the CPU time taken by our perl program. This is the si...nt “the code took, timestr($final_difference),”\n&...
2073 days ago
- ...when I went to the download directory at UCSC: http://users.s...u/admin/exe/ and that there was a linux x86_64 executabl...t part of the MACHTYPE). To correct this, in the bash shell t...npacked blat into).Now simply run the command: make to comp...
2057 days ago
