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Welcome to the Dendrome Project!

Icon 05 Resources

Scripts BLAST FASTA Readseq Galaxy Tools Databases TreeGenes Plant Ontology iPlant Downloads

Icon 03 Updates

Douglas-fir and Pinus taeda v1.0 Transcriptome loaded into GBrowse | Literature pipeline recently updated to integrate sequence data | DiversiTree custom TreeGenes interface expanded to deliver phenotype data |

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Icon 02 Links

Conifer Genome Network | Conifer Genome Project | TreeGenes Database | Dendrome Plone | Neale Lab | Forestry Careers and Education Resource |



BLAST


Basic BLAST
Use BLAST by pasting in a nucleotide or amino acid sequence in FASTA format, or simply using an accession or GI number.
  • nucleotide blast - Search a nucleotide database using a nucleotide query
    • Algorithms: blastn, megablast, discontiguous megablast
  • protein blast - Search protein database using a protein query
    • Algorithms: blastp, psi-blast, phi-blast
  • blastx - Search protein database using a translated nucleotide query
  • tblastn - Search translated nucleotide database using a protein query
  • tblastx - Search translated nucleotide database using a translated nucleotide query

[Use BLAST]



PSI-BLAST
(PSI) Position Specific Iterated BLAST - Search databases of sequence profiles to find members of the same protein family. First round runs BLAST and constructs a position-specific score matrix (PSSM) from significant hits while iterations use this PSSM as the query on profile databases. Uncovers more distant protein relationships.

[Use PSI-BLAST]



PHI-BLAST
(PHI) Pattern Hit Initiated BLAST - Identify proteins that preserve a specified pattern contained within your query. Query includes a protein sequence and a regular expression defining the pattern of interest

[Use PHI-BLAST]



BLAST 2 Sequences
Upload or paste 2 sequences and BLAST them against each other.
[Use BLAST 2 Sequences]