Genome Assembly Tools and Software - PART1 !!
The genome assemblers generally take a file of short sequenc...g a Reference Sequence The abundance of repeat elements in genomes can impede the ass...element assembler. It assembles the transposable elements directly from the raw reads....2698 days ago
Single Cell RNAseq data analysis tutorial !!
A major breakthrough (replaced microarrays) in the late 00’s and has been widely used since Measures the ...shlp.org/content/early/2016/11/18/gr.212720.116.abstract SCODE: An efficient regulato...2363 days ago
Tools for bacterial whole genome annotation
RAST – Web tool (upload contigs), uses the subsystems in the SEED databa...irect and inverted repeats, insertion sequences, transposons and other mobile elements. PGAP: NCBI has developed an...2343 days ago
PerlOneLiner for Bioinformatician
FILE SPACING------------ # Double space a fileperl -pe '$\=...l -le 'print "a"x50' # Create a repeated list of elementsperl -le '@list = (1,2)x20; pr...gth "one-liners are great"' # Find the number of elements in an arrayperl -le '@array =...2314 days ago
List of visualization tools for network biology
Network analysis is any structured technique used to mathematically analyze a circuit (a “network” of...rks Efficient integrated multi-level analysis of microarray, sequence, regulato...2300 days ago
Computational resources for TE discovery and TE detection
Transposable Elements (TEs) to genome structure and evolution as well as their impact on genome sequencing, assembly, annotation and alignment has generated increasing interes...2286 days ago
Tools to Predict the Impact of Missense Variants !
Prioritizing missense variants for further experimental investigation is a key challenge...titution affects protein function” GERP++“Identifies constrained elements in multiple alignments by qua...2215 days ago
Steps to find all the repeats in the genome !
To find repeats in a genome from 2 to 9 length using a Per...to a file containing the lengths of the reference elements. This script will genera...ntitative information about the identified repeat elements. Remember to adjust the...260 days ago