Tools

Sequence alignment
  • cmalign
  • kalign
  • clustalW/clustalX
  • MUSCLE
  • FSA
  • Diaglin-TX
  • MUMmer
Reference mapping
  • Bowtie
  • GSNAP/GSMAP
  • BLAT
  • BFAST
  • BLASER (Basic Local Alignment with Successive Refinement)
  • BWA SW: bwa bwasw database.fas ling_reads.fas > aligned.sam
Gene prediction with Introns and exons, ORF finder
  • Prokaryotics orgnisms like basteria
    • NCBI's ORF finder
  • Eukaryotic organisms like animal and plant
    • GenScan (MIT pattern scanning gene finder)
    • GeneMark (Geogia Tech's gene finder)
    • FGENSH (HHM-based gene finder from SoftBerry)
  • Checking the prediction quality of introns/exons
    • multiple sequence alignment of predicted sequences and reference sequences
    • BLAST NCBI database and find the best hit
    • multipel sequence alignment of predicted sequences with clustalW
    • check the "Kozak" consensus sequence (GccAUGG)
    • look at the intron/exon splice sites to see if they fir the "consensus" splice site sequences
  • GreenGenie2 (Washington University's Chlamydomonas-trained gene finder)
Phylogenetic analysis
  • create phylogenetic tree
    • clustalW/clustalX (Windows and Linux)
    • MEGA (Windows)
    • FASTtree
    • TECOFFE
    • HUMMER
    • Phylip
  • Bootstriping for branching stability test
  • Tree visualiztion
    • FigTree (Java program)
    • MEGA
    • TreeView
Protein structure analysis
  • Homolgy based methods
    • 3D-JIGSAW
    • Geno3D
    • MODEKKER
    • PredictProtein
    • SWISS-MODEL (ExPASy)
    • PROCHECK (quality asswssment)
    • VERIFY3D (auality assessment)
    • WHATIF (quality assessment)
  • Ab Initio prediction (template-free model)
    • i-TASSER
    • JPred 3
  • Assessment of structure prediction
    • Critical Assessment of Techniques for Protein Structure Prediction (CASP)
  • Protein structure visualization tools
    • COOT
    • Chimera
    • cn3D from NCBI
  • Protein classification
    • CATH database is a central resource fro the hiearchical classification of protein domains.
    • SCOP (Strucural Classification of Proteins) database provides a conprehensive description of protein structures and ecolutionary relationship based on a hiwarchical classification scheme. It is especially oriented towards classify whole proteins.
    • Dili Domain Dictionary: Dali (Distance matrix alignment) database provides a classification of all structures in PSB and a description of families of protein sequences associated with representative proteins of known structure.
Protein motif discovery
  • MEME for nongapped motif prediction
  • GLAM2 for gapped motif prediction
Transmembran prediction
  • HMMTOP
  • Phobius
  • TMHMM server/command line
  • MEMSAT3
  • TMPred server
RNA-Seq analysis
  • TopHat, cufflinks, and CummeRbund
  • bowtie, gsnap, BWA mapping
    • BAMtools
  • visualization of mapping and genes
    • SAVANT
    • IGV-1
    • UGENE
    • NCBI integrated genome browser
  • R package for generate gaphs
Clustering
  • nrdb2
  • CDHIT/CDHIT 454
  • UCLUST
  • gramClust
  • hclust (R heiarchical clustering package)
16S rRNA classification
  • RDP project
  • SILVA rRNA database
  • GreenGenes
  • RAST
QTL mapping
  • rQTL
Metagenomic analysis
  • BLAST
  • MEGAN
  • RAST
Gene ontology
  • DAVID web server classification of genes
  • ClueGO
  • EasyGO
  • CLENCH
  • PANTHER
Pathway analysis
  • IPA
  • KEGG
Assembly
  • AMOS
  • Velvet
  • Velvet/Clumbia for reference guided
  • ALLPATH
  • Newbler for 454 reads assembly
  • SOAP denovo
  • Euler