Wheat and its relatives:
- Triticum aestivum (bread wheat) --- IWGSC RefSeq v1.0
- Triticum urartu --- Tu2.0
- Aegilops tauschii subsp. strangulata --- Aet v4.0
- Triticum dicoccoides (wild emmer wheat) --- WEWSeq v.1.0
- Hordeum vulgare (barley) --- IBSC_v2
Peanut and its relatives:
Triticum aestivum (bread wheat) --- IWGSC RefSeq v1.0
Genome: AABBDD Cultivar: Chinese Spring
Analysed the IWGSC RefSeq v1.0
assembly
using TRF Version 4.09, the main parameters are: 2 7 7 80 10 50 2000.
Then non-redundant TR arrays (Percent Matches ≥ 80) were filtered out by an in house script, the flow is shown
in flow-to-get-NR-TR-arrays.pdf.
Files
Query
Triticum urartu --- Tu2.0
Genome: AA Cultivar: G1812
Analysed the Tu2.0
assembly
using TRF Version 4.09, the main parameters are: 2 7 7 80 10 50 2000.
Then non-redundant TR arrays (Percent Matches ≥ 80) were filtered out by an in house script, the flow is shown
in flow-to-get-NR-TR-arrays.pdf.
Files
Query
Aegilops tauschii subsp. strangulata --- Aet v4.0
Genome: DD Cultivar: AL8/78
Analysed the
Aet v4.0
assembly
using TRF Version 4.09, the main parameters are: 2 7 7 80 10 50 2000.
Then non-redundant TR arrays (Percent Matches ≥ 80) were filtered out by an in house script, the flow is shown
in flow-to-get-NR-TR-arrays.pdf.
Files
Query
Triticum dicoccoides (wild emmer wheat) --- WEWSeq v.1.0
Genome: BBAA Ecotype: Zavitan
Analysed the WEWSeq v.1.0
assembly
using TRF Version 4.09, the main parameters are: 2 7 7 80 10 50 2000.
Then non-redundant TR arrays (Percent Matches ≥ 80) were filtered out by an in house script, the flow is shown
in flow-to-get-NR-TR-arrays.pdf.
Files
Query
Hordeum vulgare --- IBSC_v2
Genome: HH Cultivar: Morex
Analysed the
IBSC_v2
assembly
using TRF Version 4.09, the main parameters are: 2 7 7 80 10 50 2000.
Then non-redundant TR arrays (Percent Matches ≥ 80) were filtered out by an in house script, the flow is shown
in flow-to-get-NR-TR-arrays.pdf.
Files
Query
Arachis hypogaea (cultivated peanut) --- Tifrunner.gnm1.KYV3
Genome: AABB Cultivar: Tifrunner
Analysed the Tifrunner.gnm1.KYV3
assembly
using TRF Version 4.09, the main parameters are: 2 7 7 80 10 50 2000.
Then non-redundant TR arrays (Percent Matches ≥ 80) were filtered out by an in house script, the flow is shown
in flow-to-get-NR-TR-arrays.pdf.
Files
Query
Arachis duranensis --- V14167.gnm1.SWBf
Genome: AA Cultivar: V14167
Analysed the V14167.gnm1.SWBf
assembly
using TRF Version 4.09, the main parameters are: 2 7 7 80 10 50 2000.
Then non-redundant TR arrays (Percent Matches ≥ 80) were filtered out by an in house script, the flow is shown
in flow-to-get-NR-TR-arrays.pdf.
Files
Query
Arachis ipaensis --- K30076.gnm1.bXJ8
Genome: BB Cultivar: K30076
Analysed the K30076.gnm1.bXJ8
assembly
using TRF Version 4.09, the main parameters are: 2 7 7 80 10 50 2000.
Then non-redundant TR arrays (Percent Matches ≥ 80) were filtered out by an in house script, the flow is shown
in flow-to-get-NR-TR-arrays.pdf.
Files
Query
Arachis hypogaea (cultivated peanut) --- ASM371315v1 (Shitouqi)
Genome: AABB Cultivar: Shitouqi
Analysed the ASM371315v1
assembly (data downloaded from The Peanut Genome Resource)
using TRF Version 4.09, the main parameters are: 2 7 7 80 10 50 2000.
Then non-redundant TR arrays (Percent Matches ≥ 80) were filtered out by an in house script, the flow is shown
in flow-to-get-NR-TR-arrays.pdf.
Files
Query
Update log:
- No longer only limited to wheat and its relatives.