Data and Sources

Brassicaceae

• Comparative Evolution (CoGe)

  • https://genomevolution.org/coge/

• EnsemblPlants

  • http://plants.ensembl.org/Arabidopsis_thaliana/Info/Index

  • http://plants.ensembl.org/Multi/Search/Results/species_plants?db=core;q=arabidopsis;species=all;collection=all;site=ensemblunit;

  • http://plants.ensembl.org/Multi/Search/Results?species=all;idx=;q=NRPD1B;site=ensemblunit

  • http://plants.ensembl.org/Multi/Search/Results?species=all;idx=;q=KTF1;site=ensemblunit

• Phytozome

  • http://www.phytozome.net/

• Salk Institute Genomic Analysis Laboratroy (SIGnAL)

  • http://signal.salk.edu/

  • http://signal.salk.edu/atg1001/index.php

• 1001 Genomes

  • http://1001genomes.org/

Oryzeae

• Comparative Evolution (CoGe)

• EnsemblPlants

  • http://plants.ensembl.org/Oryza_sativa/Info/Index

  • http://plants.ensembl.org/Multi/Search/Results/species_plants?db=core;q=oryza;species=all;collection=all;site=ensemblunit;

• GigaScience database (GigaDB)

  • http://www.gigasciencejournal.com/content/3/1/7

• National Center for Biotechnology Information (NCBI) database biosample for 3000 genomes project

  • http://www.ncbi.nlm.nih.gov/biosample?Db=biosample&DbFrom=bioproject&Cmd=Link&LinkName=bioproject_biosample&LinkReadableName=BioSample&ordinalpos=1&IdsFromResult=262761

• OryzaSNP

  • http://oryzasnp.org/iric-portal/

• Rice Annotation Project Database (RAP-DB)

  • http://rapdb.dna.affrc.go.jp/index.html

• Rice Genome Annotation Project (RGAP) 

  • http://rice.plantbiology.msu.edu

• 3k RGP and OryzaSNP data repository

  • http://oryzasnp-atcg-irri-org.s3-website-ap-southeast-1.amazonaws.com/

Programs

AGO Hook Identification

• Self-generated python scripts

  • Available on my GitHub account

    • https://github.com/J3TT/PLS-599-Homework

• Identifies AGO Hooks within a protein sequence

• Requirements to run...

  • FASTA file with sequence(s) of interest

DnaSP

• Software of analyzing DNA sequence polymorphisms (SNPs)

  • http://www.ub.edu/dnasp

• Requirements to run...

  • Alignment file containing sequences of interest

Genome Analysis Toolkit (GATK)

• Offer by Broad Institute

  • https://www.broadinstitute.org/gatk/

  • https://www.broadinstitute.org/gatk/guide/tooldocs/

• FASTA file converter/maker

  • https://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_gatk_tools_walkers_fasta_FastaAlternateReferenceMaker.php

• Software for analyzing high-throughput next-gen sequencing data

• Requirements to run...

InterPro Scan

• Offered by EMBL-EBI

  • http://www.ebi.ac.uk/Tools/webservices/services/pfa/iprscan5_soap

    • RADAR Script

      • http://www.ebi.ac.uk/Tools/webservices/download_clients/python/soappy/iprscan5_soappy.py

• Identifies known domains within a protein of interest

• Requirements to run...

  • Installation of SOAPpy, PyXML,  and fpconst Python Modules

• All modules downloaded and used available from python** https://pypi.python.org/pypi?%3Aaction=index

LAST

• Offered by Computational Biology Research Center (CBRC)

  • http://last.cbrc.jp?

• Homology search tool

• Requirements to run...

  • FASTA files of sequences to be aligned/searched