I am going to compare bacterial genomes to find structure of some interesting genes and design primers for the target genes.
It all depends on your goals. I'd start with a linux box. Here are some basic tools installed on mine:
BIOPIECES : OK
subversion client - "svn: OK
PERL : OK
PERL:Inline : OK
PERL:JSON::XS : OK
PERL:SVG : OK
PERL:Bit::Vector : OK
PERL:Time::HiRes : OK
Ruby : OK
RubyGem:gnuplot : OK
RubyGem:narray : OK
RubyGem:RubyInline : OK
RubyGem:Bio-blastxmlparser: ?
blastall : OK
blat : OK
bwa : OK
bowtie : OK
formatdb : OK
gnuplot : OK
idba : WARNING
muscle : OK
mummer : OK
mysql : OK
prodigal : OK
Ray : OK
scan_for_matches : WARNING
usearch : WARNING
velveth : OK
velvetg : OK
vmatch : WARNING
PAGIT : OK
Artemis : OK (nnotation & BAM visualization tool - version Dec2011)
ACT : OK (DNA sequence comparison viewer v. Dec2011)
BLASTALL : OK (Blast version 2.2.15)
MUMmer : OK (sequence comparison tools - version 3.22)
SAMTOOLS : OK (short read mapper BAM/SAM files) version 1.0.19
SMALT : OK (read mapping tool (k-mer based) - version 0.5.3)
VELVET : OK (short read assembler - version 1.1.06)
FastQC : OK (qality assess fastq file)
fastx-toolkit 0.0.12 : OK
Homer Tools : OK
Bioperl : OK
Biopython : OK
Ray 2.2.0 : OK (assembler)
usearch : OK
Bowtie2 2-2.1.0 : OK (read mapper)
CAP3 : OK (long read assembler)
Jellyfish : OK (k-mer counting)
ea-utils.1.1.2-537 : OK (adapterscan, demultiplex, and joining fastq files)
SSPACE : OK (extend contigs of assembly using paired end reads)
Cython : OK
Pysam : installed (untested)
SciPy : OK
NumPy : OK
EMIRGE : installed (untested)
ncbi-blast-2.2.28+ : OK
HMMER 3.0 : installed (untested)
MEGAN 4 : OK
multi-metagenome : deployed (untested; not in path)
Rstdudio : OK
R : OK
R(knitr) : OK
R(vegan) : OK
R(plyr) : OK
R(RColorBrewer) : OK
R(alphahull) : OK
R(ggplot2) : OK
Hi
You can use ACT from Sanger to compare genomes. Didactic and easy!!!
For comparison of WGS data, you can use tools like Mauve, MUMMER, BLAST, ACT (Artemis Comparison Tool), etc.
I am not sure what your goal is.
You wish to compare whole genome sequences to predict structures and design primers for the genes?
I mean, what genes are you targeting specifically?
What do you mean by gene structures?
- Badges
- Science topic
- Similar topics
- Biological Science
- Molecular Biology
- Molecular Biological Techniques