Software available on molbiol

The following bioinformatics packages are available to molbiol account holders on our server, orac:

AceDB - a tool for viewing and managing genomic data
- External link: www.acedb.org
- Example command line:
xace .

Artemis / ACT - Artemis: genome viewer and annotation tool, and ACT: (Artemis Comparison Tool) a DNA sequence comparison viewer based on Artemis
- External link: www.sanger.ac.uk/Software/Artemis
- Example command lines:
art genome.gbk
act genome1.gbk genome1_genome2.blastresults genome2.gbk

Bioconductor - Bioconductor is an open source and open development software project for the analysis and comprehension of genomic data. Bioconductor is primarily based on the R programming language
- External link: www.bioconductor.org/

BLAST - Basic Local Alignment Search Tool for sequence similarity searching against nucleotide and protein databases
- More details: BLAST
- External link: www.ncbi.nlm.nih.gov/BLAST
- Example command line:
blastall -p blastp -d ensembl_human_pep -i myqueryseq.fasta -o blast.out

bl2seq - compare two sequences using BLAST (both sequences either protein or nucleotide)
- Example command line:
bl2seq -i seq1.fasta -j seq2.fasta -p blastn -o bl2seq.results

ClustalW - multiple sequence alignment program for DNA/proteins. Graphic interface, ClustalX, also available
- Example command line:
clustalw -align -infile=seqs.fasta -type=dna

EMBOSS - a suite of more than 100 bioinformatics tools
- Also on the web at: EMBOSS

FASTA - Sequence similarity searching against nucleotide and protein databases
- Example command lines:
fasta -q -S sequence.fasta /databank/raw/uniref90/uniref90.fasta
fasta -q -S sequence.fasta /databank/raw/genbank/gbsts*
- Databases: FASTA files available for searching on orac can be found at: /databank/raw/
- Note: The FASTA files for NCBI sequences (i.e. nr, nt, est, sts, env & pat) are not available. However, FASTA can search the equivalent BLAST databases, for example:
fasta -q -S sequence.fasta -l $BLASTDB/nt*

formatdb - Prepare a nucleotide or protein sequence file for seaching using BLAST
- More details: Formatdb
- External link: www.ncbi.nlm.nih.gov/BLAST/docs/formatdb.html
- Example command line:
formatdb -p F -o T -i all_seqs.fasta -n customBLASTdb

Glimmer - (Gene Locator and Interpolated Markov Modeler) a system for finding genes in microbial DNA, especially the genomes of bacteria, archaea, and viruses.
- External link: www.tigr.org/software/glimmer
- Example command lines (analysis carried out in four steps):
long-orfs genome.fasta > genome.long_orfs
extract genome.fasta genome.long_orfs > genome.extract
build-imm < genome.extract > genome.imm
glimmer2 genome.fasta genome.imm

GENSCAN - predicts the locations and exon-intron structures of genes in genomic DNA
- External link: http://genes.mit.edu/GENSCAN.html
- Example command line:
genscan /package/genscan/1.0/lib/HumanIso.smat genome.fasta

HMMER - Profile hidden Markov models software for protein sequence analysis.
- External link: http://hmmer.wustl.edu/

Jalview - a multiple sequence alignment editor written in java
- External link: http://www.jalview.org/
- Example command line (alignment files must be one of: CLUSTAL, FASTA, MSF, PIR or BLC):
jalview seqs.aln File CLUSTAL

MeV - TIGR MultiExperiment Viewer (MeV) is a Java application designed to allow the analysis of microarray data to identify patterns of gene expression and differentially expressed genes.
- External link: www.tm4.org/mev.html
- Example command line:
tmev

mfold - DNA/RNA secondary structure prediction
- External link: www.bioinfo.rpi.edu/~zukerm/seqanal/mfold-3.0-manual.pdf
- Example command lines (note: the mfold environment must be set up first using "usepkg"):
usepkg mfold
mfold SEQ=glld.seq

MSPcrunch - a BLAST output filtering tool
- External link: www.cgb.ki.se/cgb/groups/sonnhammer/MSPcrunch.html
- Example command line:
MSPcrunch -P -e 1e-50 sequence_blast.outout

MUMmer - a system for rapidly aligning entire genomes
- External link: www.tigr.org/software/mummer
- Example command line:
mummer -mum -b -c genome1.fasta genome2.fasta > genomes_mummer.out
- this data can be plotted:
mummerplot --postscript -p=genomes_mumplot genomes_mummer.out
gnuplot genomes_mumplot.gp

OligoArray - computes gene specific oligonucleotides for genome-scale oligonucleotide microarray construction
- External link: http://berry.engin.umich.edu/oligoarray2_1
- Example command line (NB. case sensitive):
OligoArray2 -i sequence.fasta -d ens_human_cdna

Phred, Phrap and Consed - Phred: reads DNA sequencing trace files, calls bases, and assigns a quality value to each called base; Phrap: assembles shotgun DNA sequence data using the base calls and base quality values produced by Phred; Consed: a tool for viewing, editing, and finishing sequence assemblies created with Phrap
- External link: www.phrap.org

Phylip - package of programs for inferring phylogenies.
- External link: http://evolution.genetics.washington.edu/phylip/general.html

Phylodendron - draws phylogenetic trees for use in evolutionary biology.
- External link: http://iubio.bio.indiana.edu/soft/molbio/java/apps/trees/phylodendron-doc.html

Primer3 - design primers within a DNA sequence
- External link: http://frodo.wi.mit.edu/primer3/primer3_code.html
- Example command line:
primer3_core -format_output -2x_compat -strict_tags < sequence.IO
- Note: input sequence must be BOOULDER_IO format. All optional parameters used by primer3 (e.g. PRIMER_PRODUCT_SIZE_RANGE=100-300 PRIMER_GC_CLAMP=1 PRIMER_OPT_SIZE=22) are included in this input file - further details at: http://frodo.wi.mit.edu/primer3/README.primer3_1.0.0

R - a software environment for statistical computing and graphics. Provides a wide variety of statistical (linear and nonlinear modelling, classical statistical tests, time-series analysis, classification, clustering, ...) and graphical techniques, and is highly extensible
- External link: www.r-project.org/

RepeatMasker - screens DNA sequences for interspersed repeats and low complexity DNA sequences
- External link: www.repeatmasker.org
- Example command line:
RepeatMasker sequence.fasta

Readseq - reads sequence files and interconverts between many different sequence file formats
- External link: http://iubio.bio.indiana.edu/soft/molbio/readseq/version2/Readseq2-help.html
- Example command line:
readseq run -f8 sequence.gbk -o sequence.fasta

RSmatch - comparison of RNS structures
- External link: http://exon.umdnj.edu/software/RSmatch/
- Example command line:
RSmatch -p dsearch -D all_apts.fasta -Q test_apt.fasta -r 1 -W 120

SeaView - a graphical multiple sequence alignment editor. Reads and writes various alignment formats (NEXUS, MSF, CLUSTAL, FASTA, PHYLIP, MASE). In addition to manual editing, it allows running of DOT-PLOT or CLUSTALW to locally improve the alignment
- External link: http://pbil.univ-lyon1.fr/software/seaview.html
- Example command line:
seaview seqs.aln

Sequin - stand-alone software tool developed by the NCBI for submitting and updating entries to the GenBank, EMBL, or DDBJ sequence databases.
- External link: www.ncbi.nlm.nih.gov/Sequin/
- Example command line:
sequin

sim4 - aligns an expressed DNA sequence (EST, cDNA, mRNA) with a genomic sequence for the gene
- External link: http://globin.cse.psu.edu/html/docs/sim4.html
- Example command line:
sim4 transcript_seq.fasta genome_seq.fasta

SRS - (Sequence Retrieval System) for database and cross-database querying
- Web interface: https://zen.molbiol.ox.ac.uk/srs-7.1.3.1/cgi-bin/wgetz?-page+srsq2+-noSession
- Example command lines:
getz -libs
getz "[embl:humtk]" -e

Staden - a set of DNA sequence assembly, editing and analysis tools
- External link: http://staden.sourceforge.net
- Example command lines:
trev &
pregap4 &
gap4 &

STARS - an alternative interface to Staden for sequence assembly of sequence typing projects
- External link: www.cbrg.ox.ac.uk/~mchan/stars/

T-COFFEE - a DNA or protein multiple sequence alignment package
- External link: http://igs-server.cnrs-mrs.fr/~cnotred/Projects_home_page/t_coffee_home_page.html
- Example command line:
t_coffee seqs.fasta

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