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Published Histories | pavel | workshop_TEdomains
Import history

Galaxy History ' workshop_TEdomains'


DatasetAnnotation
1: input.fasta
9,729 sequences
format: fasta, database: ?
Info: uploaded fasta file
>CL1Contig1 (815-1.9-1535)
TTCCCCGACATCTTTGGCGCGCCAGGTAGGGGGGTGCGTCGAGATTGTGTGAACCCGATC
CGGCGTCCACACGAGCCAGATCTTCATCGTCTTCATCAACATGCCGCCGAAGAAGAAGGC
TTTGGAGGTAGCTGGACCGTCCGCGTCGATCCCACCACCGCCAGAGCCAACGGCTGGTGG
GGTAGACGCCGGAAGAAGAACGGACATCGACGAGGGAACTCACGGTGCTGCCAGGTCCAA
GGGCAAGGCTAGCGTAGCCGGCTCCCACGACGACCGGGCACACTCCAAGACCTCGGCATC
2: Protein domain search on dataset 1
219,544 lines
format: fasty36, database: ?
fasty36 -m 3 -m9 -b 1 -H -q -O output.part.0 - /home/galaxy/galaxy-dist/tool-data/domains/TE_domains_newest_RT
FASTY compares a DNA sequence to a protein sequence data bank version 36.06 Sep, 2010
Please cite:
Pearson et al, Genomics (1997) 46:24-36
Query: CL1Contig1, 815 aa
3: Ty1 domains from dataset-2
45 sequences
format: fasta, database: ?
Info: keys: Ty1-RT__Wicker_Osr1_Os_cons

Ty1-RT__Wicker_Barbara_A_210J24-3

Ty1-RT__Wicker_Inga_AY661558-2

Ty1-RT__Wicker_Angela_A_cons

Ty1-RT__Wicker_Inga_AY661558-2

Ty1-RT__Wicker_BARE1_B_cons

Ty1-RT__Wicker_Angela_A_cons

Ty1-RT__Wicker_WIS_B_cons
>CL27Contig4_592-1236
WIQAMQEELQQFELNNVWELVKRPDPRKHNIIGTKWIYRNKQDEHGQVVR
NKARLVAQGYTQVEGIDFDETFAPVARLEAIRILLAYANHHNIFLYQMDV
KSAFLNGKIEEEVYVAQPPGFEDPKRPDMVYKLNKALYGLKQAPRAWYDT
LKDFLKSKGFKPGSLDPTLFTKTYDGELFVCQIYVDDIIFGCTVKRYSYE
FGYMMQVQYQMSMMG
4: Ty3 domains from dataset-2
106 sequences
format: fasta, database: ?
Info: keys: Ty1-RT__Wicker_Osr1_Os_cons

Ty1-RT__Wicker_Barbara_A_210J24-3

Ty1-RT__Wicker_Inga_AY661558-2

Ty1-RT__Wicker_Angela_A_cons

Ty1-RT__Wicker_Inga_AY661558-2

Ty1-RT__Wicker_BARE1_B_cons

Ty1-RT__Wicker_Angela_A_cons

Ty1-RT__Wicker_WIS_B_cons
>CL1Contig12_3035-3556
VRGVIHPTWLANPVVVRKANGKWRLCIDFTDVNKACPKDPFPLPRIDQIV
DSTAGCELLSFLDAYSGYHQIFMAKEDEEKTAFITPCGTYCFIRMPFGLK
NAGSTFARVVYTAFEPQIHRNVEAYMDDIVVKSKSKETLIQDLEETFQNL
RRIQLKLNPEKCVFGVPSGKLLGF
>CL1Contig13_3060-3581
5: Parsed and filtered fasty36 results from dataset 2
131 lines
format: tabular, database: ?
Info: keys: Ty1-RT__Wicker_Osr1_Os_cons

Ty1-RT__Wicker_Barbara_A_210J24-3

Ty1-RT__Wicker_Inga_AY661558-2

Ty1-RT__Wicker_Angela_A_cons

Ty1-RT__Wicker_Inga_AY661558-2

Ty1-RT__Wicker_BARE1_B_cons

Ty1-RT__Wicker_Angela_A_cons

Ty1-RT__Wicker_WIS_B_cons
12345678910111213141516171819202122232425
Typelineagequery_namequery_lengthhit_namehit_lengthstrandoptsbitse_valperc_idperc_simswalenan0ax0pn0px0an1ax1pn1px1gapqgaplfs
Ty3/gypsyOgre/TatCL1Contig124659Ty3-RT__RIRE2_I174f878243.62.2e-650.6780.874878174303535561465911741174000
Ty3/gypsyOgre/TatCL1Contig134492Ty3-RT__RIRE2_I174f8942481.1e-660.690.885894174306035811449211741174000
Ty3/gypsyOgre/TatCL1Contig235275Ty3-RT__RIRE2_I174f878243.72.5e-650.6780.874878174330138221527511741174000
Ty3/gypsyOgre/TatCL1Contig263906Ty3-RT__RIRE2_I174f897248.85.3e-670.6950.885897174289134121390611741174000
Ty3/gypsyOgre/TatCL1Contig27663Ty3-RT__RIRE2_I174r840233.34.1e-630.6780.87984017458461663111741174002
6: Aligment from-dataset 4
678 lines
format: msf, database: ?
PileUp
MSF: 198 Type: A Check: 0000 ..
Name: CL3472Contig1_495-48 Len: 198 Check: 9509 Weight: 0.00257114
Name: Ty3-RT__Reina_ZeaM_ID49 Len: 198 Check: 2348 Weight: 0.00219491
7: Tree in Newick format from dataset 4
1 line
format: newick, database: ?
((((((CL22Contig45_1536-2057:1.582044752,CL22Contig29_1387-1908:0.137955248):2.053871496,CL22Contig42_1380-1901:0.2461285037):0.4927109697,CL22Contig59_300-821:0.6572890303):0.2022996261,CL22Contig28_1370-1874:5.607700374):0.5295751272,(CL22Contig4_3387-29
08:2.948046482,CL22Contig52_224-740:5.181953518):1.475737373):1.369706055,((((((CL3886Contig1_248-691:9.167816577,CL22Contig15_104-556:7.732183423):1.170535244,((((((((CL145Contig3_508-1030:4.099745577,CL145Contig5_167-688:1.070254423):1.59827643,CL1086Con
tig1_216-737:4.43672357):12.22750581,(CL86Contig2_3068-2547:0.8382326434,CL86Contig3_981-1421:4.601767357):15.95374419):1.398933321,(((((((CL483Contig1_742-221:2.192095571,CL48Contig11_3010-3531:1.827904429):1.034921588,CL942Contig1_549-1023:8.665078412):0
.9469016104,CL48Contig21_785-272:7.99059839):3.095032985,CL1368Contig1_1-441:9.499967015):0.2992858347,(((((CL1Contig26_2891-3412:0,CL1Contig33_2030-2551:0):0.254273306,CL1Contig13_3060-3581:0.315726694):0.7217059939,(CL1Contig23_3301-3822:0.3119351248,CL1
Contig27_584-61:0.2580648752):1.005794006):0.773911109,CL1Contig38_1592-2113:3.824838891):0.1900938936,(((CL1Contig39_1020-514:0.7109930526,CL1Contig51_2075-1554:-0.1209930526):0.3061135159,CL1Contig31_2494-3015:0.2738864841):0.9670053843,(CL1Contig12_3035
-3556:0.03863205501,CL1Contig30_1298-1819:0.531367945):1.062994616):0.8234998564):4.279112603):7.870060161,((((CL2331Contig1_3-525:7.324228841,CL999Contig1_343-862:5.395771159):1.270599902,CL1828Contig1_767-246:9.084400098):1.782835962,CL142Contig3_1078-16
8: Neighbor joining tree from dataset 4
60.2 KB
format: html, database: ?
HTML file
10: filtered fasty36 output from dataset 2, (min.similarity 60, min.identity 40, max.frameshifts 3)
131 lines
format: tabular, database: ?
1234567891011121314151617181920212223242526
"Type""lineage""query_name""query_length""hit_name""hit_length""strand""opts""bits""e_val""perc_id""perc_sim""sw""alen""an0""ax0""pn0""px0""an1""ax1""pn1""px1""gapq""gapl""fs""sequence"
"Ty3/gypsy""Ogre/Tat""CL1Contig12"4659"Ty3-RT__RIRE2_I"174"f"878243.62.2e-650.6780.874878174303535561465911741174000"GTTAGAGGCGTGATCCATCCGACGTGGTTAGCAAATCCAGTCGTCGTGCGTAAGGCCAACGGGAAGTGGAGACTGTGTATAGACTTCACCGATGTGAATAAAGCATGTCCCAAG
GATCCATTTCCCTTGCCGCGCATTGACCAGATTGTTGACTCCACTGCCGGATGTGAGCTACTCTCTTTTCTTGATGCATATTCAGGCTACCACCAGATTTTCATGGCCAAGGAAGATGAAGAGAAGACTGCATTTATCACTCCATGTGGCACTTATTGCTTCATACGCATGCCATTTGGACTGAAGAATGCAGGCTCAACTTTTGCAAGGGTAGTGTACACTGCTTTTGAGCCACAGATCCACAGAAATGTAGAAG
CTTACATGGATGACATCGTGGTGAAGAGCAAGAGCAAAGAAACACTGATTCAAGACTTGGAAGAAACGTTTCAGAACCTGCGCAGGATACAGCTCAAGCTGAACCCCGAGAAGTGCGTCTTTGGAGTTCCCTCCGGCAAGCTTCTCGGGTTC"
"Ty3/gypsy""Ogre/Tat""CL1Contig13"4492"Ty3-RT__RIRE2_I"174"f"8942481.1e-660.690.885894174306035811449211741174000"GTTAGAGGCGTAATACATCCCACGTGGTTGGCCAATCCAGTTGTCGTGCGAAAGGCTAATGGAAAGTGGAGACTTTGTATAGACTTCACCGACGTGAACAAAGCTTGTCCCAAGGAT
CCCTTTCCCTTGCCGCGCATCGACCAAATTGTTGACTCCACAGCTGGATGTGAGTTGCTCTCATTCCTTGATGCATACTCAGGTTACCACCAGATATTCATGGCCGAGGAAGATGAAGAGAAGACTGCATTCATTACTCCATGTGGCACATATTGCTTCATACGCATGCCCTTTGGATTGAAGAATGCGGGCTCAACATTTGCAAGGGTGGTCCACACTGCTTTTGAGCCACAGATACACAGGAATGTAGAAGCCT