Methods & Sources


Pv_bat93_alignments

HSP Alignments of Phaseolus vulgaris genotype bat93 reads to Glycine max using ab-blast (-e 1e-3 -topcomboN 10 -hspsepSmax 50000 -golmax 15).

For BAT93 reads:

This data is free; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version.

Pv_ssr_predictions

SSR predictions using ssrit, ssr_finder, and QDD.

Options for ssrit:

  • 2-nt motif, >= 7 repeats
  • 3-nt motif, >= 7 repeats
  • 4-nt motif, >= 7 repeats
  • 5-nt motif, >= 7 repeats
  • 6-nt motif, >= 7 repeats

Options for ssr_finder: All motifs, at least 7 repeats

Options for QDD:

  • 0: Operating system (win/linux): linux
  • 1: Input folder: data
  • 2: Delete intermediate files (YES=1/NO=0): 1
  • 3: Sort sequences by tag (YES=1/NO=0): 0
  • 4: Remeove adapter (YES=1/NO=0): 0
  • 5: Minimum sequence length: 10
  • 6: Minimum number of monobase repetitions in MS search: 10000000
  • 7: Minimum number of dibase repetitions in MS search: 7
  • 8: Minimum number of tribase repetitions in MS search: 7
  • 9: Minimum number of tetrabase repetitions in MS search: 7
  • 10: Minimum number of pentabase repetitions in MS search: 7
  • 11: Minimum number of hexabase repetitions in MS search: 7
  • 12: Pathway to BLAST: /share/apps/blast/bin/

The top two hits of each SSR were mapped to G. max using ab-blast (-e 1e-3 -topcomboN 10 -hspsepSmax 50000 -golmax 15). Blue is the top hit, orange is the 2nd hit.

Pv_BAT93_assembly

Assembly mapped to G. max using ab-blast.

Methods: Described in Timko et al. 2008 Information provided by M. Timko (University of Virginia)
Timko MP, Rushton PJ, Laudeman TW, Bokowiec MT, Chipumuro E, Cheung F, Town CD, Chen X (2008) Sequencing and analysis of the gene-rich space of cowpea. BMC Genomics 9:Article No.: 103

bat93_hsp_evalue

Continuous data track showing average (-log) evalues of aligned Pv HSPs to G. max. Data extracted using sliding window of 1000bp.

bat93_hsp_evalue_100000

Continuous data track showing average (-log) evalues of aligned Pv HSPs to G. max. Data extracted using sliding window of 100000bp

scar_markers_new

SCAR markers aligned to G. max using ab-blast.
Reference: Miklas P. SCAR markers linked with disease resistance traits in common bean (Phaseolus vulgaris). December 2010 update.

ssr_markers_new

SSR Markers aligned to G. max using ab-blast. References: Yu et al.
2000b, Grisi et al. 2007, Buso et al. 2006, Cardoso et al. 2008,
Gaitan-Solis et al. 2002, Blair et al. 2003, Blair et al. 2009

sts_markers_new

STS Markers aligned to G. max using ab-blast. References: Murray et al. 2002, Hougaard et al. 2008, McConnell et. al., 2010 McConnell M, Mamidi S, Lee R, Chikara S, Rossi M, Papa R, McClean P (2010) Syntenic relationships among legumes revealed using a gene-based genetic linkage map of common bean (Phaseolus vulgaris L.). Theor Appl Genet 121:1103-1116

other_markers_new

Other markers aligned to G. max using ab-blast. References: Kim et al., 2006.
Kim D-J, Kaur M, Ferguson M (2006) COS marker development in cowpea-beans. Generation Challenge Program

Various markers

Jan Brazolot & Peter Pauls, Guelph U.; Jim Kelly, Michigan State University; Phil McClean, North Dakota State University; Phil Miklas & Richard Larsen, USDA-ARS, Prosser, WA;
Thiago L. P. O. de Souza, Everaldo de Barros & Maurilio Moreira, Universidade Federal de Viçosa, Brasil; Kangfu Yu, Agriculture Canada, Greenhouse and Processing Crops Research Centre, Ontario, Canada

All Soybase tracks

pv_jcvi_2, pv_mcclean, pv_bac_clones, vigna_unguiculata, cowpea_gsr_reads, cowpea_assembly, glyma1, old_duplication_blocks, recent_duplication_block, synteny_blocks_to_medicago, phaseolus_coccineus_2
Soybase citations

Predicted Primers

Predicted primers were generated using Primer3 using the following settings file with particular attention to the SEQUENCE_ID, SEQUENCE_TEMPLATE, SEQUENCE_TARGET, SEQUENCE_EXCLUDED_REGION lines.

Blasts

Soybean hits found and pre-generated for the database were found using ABBlast with the following custom parameters:

-e 1e-3 -topcomboN 10 -hspsepSmax 50000 -golmax 15

Custom blasts performed on this site are done using NCBI blastn blast with default settings and e-value cutoff 0.0001. The Phaseolus Vulgaris 1.0 database comes from Phytozome (Aug 27, 2012).

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