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Project Description

The aim of this project is to create an automated pipeline for taxonomic assignment of DNA sequences obtained from environmental samples.

We develop a series of python scripts to process the raw sequence data obtained from benthic environmental samples and to taxonomical assignment of these sequences and finally to integrate all data in a relational database.

System Requirements

System requirement is not defined

Download Package list

Latest 5 files
Name Size Date Download count
2012-02-16.txt 64.5 KB 2012-07-25 21:06 2
2012-02-14.rtf 6.3 KB 2012-07-25 21:05 1
2012-02-10_blastparse.rtf 1.5 KB 2012-07-25 21:05 2
MySQL create_modify table.eml 1.8 KB 2012-07-25 21:02 5
plos figure.eml 48.1 KB 2012-07-25 21:02 4
All Files
KTH_Project
Minttus notebook
2012-02-16.txt64.5 KB2012-07-25 21:062
2012-02-14.rtf6.3 KB2012-07-25 21:051
2012-02-10_blastparse.rtf1.5 KB2012-07-25 21:052
MySQL create_modify table.eml1.8 KB2012-07-25 21:025
plos figure.eml48.1 KB2012-07-25 21:024
Regexp explanation.eml4.3 KB2012-07-25 21:020
Re_ may be of use....eml18.8 KB2012-07-25 21:022
Re_ NCBI taxonomy.eml19.5 KB2012-07-25 21:020
Re_ Summary-of-Trawl-2-Phyla-by-cluster-csv.csv (c6h5cho@gmail.com).eml8.5 KB2012-07-25 21:024
To do list for Bioinformatics project.eml3.3 KB2012-07-25 21:023
Trawl 4 Blast results and Phyla by cluster (sarah.bourlat@gmail.com).eml5.5 KB2012-07-25 21:028
bioseqdb query.eml2.7 KB2012-07-25 21:025
BioSQL database commands.eml18.9 KB2012-07-25 21:021
Biosql database design.eml13.3 KB2012-07-25 21:024
BioSQL database update.eml8.7 KB2012-07-25 21:021
BioSQL design notes.eml8.5 KB2012-07-25 21:022
BLASTX command-line 1.eml44.8 KB2012-07-25 21:020
BLASTX command-line .eml44.8 KB2012-07-25 21:024
from blast to sql.eml4.2 KB2012-07-25 21:023
Fwd_ Entering the biosql database.eml29.1 KB2012-07-25 21:020
Fwd_ Sequence clustering tests before and after removal of ambitious bases.eml66.2 KB2012-07-25 21:021
Here are the revised figures.eml90.4 KB2012-07-25 21:023
How to query the SQL database.eml1.4 KB2012-07-25 21:021
Joining two SQL queries.eml9.4 KB2012-07-25 21:024
Labbook entry_ Notes on populating the biosql database.eml8.1 KB2012-07-25 21:023
Bioinformatics project update 29.01.2012.eml7.4 KB2012-07-25 21:024
2012-01-191.6 KB2012-07-25 21:022
2012-01-160.8 KB2012-07-25 21:024
2012-01-101.6 KB2012-07-25 21:021
2012-01-060.8 KB2012-07-25 21:021
2012-01-052.0 KB2012-07-25 21:021
2011-12-14 projectoutline.pdf64.8 KB2012-07-25 21:0226
2.eml4.2 KB2012-07-25 21:021
1.eml2.6 KB2012-07-25 21:023
2012-01-11.txt1.0 KB2012-07-25 20:456
2012-01-261.4 KB2012-07-24 23:061
2012-02-155.7 KB2012-07-24 23:040
2012-02-015.1 KB2012-07-24 22:513
2012-01-221.7 KB2012-07-24 22:513
bash_0501127.7 KB2012-07-23 05:095
bash_06011228.8 KB2012-07-23 05:090
bash_060112.21.9 KB2012-07-23 05:090
bash_09011216.0 KB2012-07-23 05:091
bash_090112.225.8 KB2012-07-23 05:091
bash_15121110.3 KB2012-07-23 05:098
bash_10011219.3 KB2012-07-23 05:090
bash_151211.2119.8 KB2012-07-23 05:090
bash_100112.225.5 KB2012-07-23 05:093
bash_14011215.0 KB2012-07-23 05:091
bash_30011218.6 KB2012-07-23 05:093
bash_31011227.2 KB2012-07-23 05:093
bash_01021246.7 KB2012-07-23 05:090
bash_02021265.3 KB2012-07-23 05:094
bash_0802121.2 MB2012-07-23 05:092
bash_100212108.8 KB2012-07-23 05:096
bash_170212156.6 KB2012-07-23 05:095
bash_170212.2223.2 KB2012-07-23 05:090
bash_170212.3116.7 KB2012-07-23 05:095
bash_18021237.9 KB2012-07-23 05:094
bash_240212450.8 KB2012-07-23 05:095
bash_270212781.6 KB2012-07-23 05:091
bash_13061253.7 KB2012-07-23 05:091
Sarahs notebook
Trawl 4 Blast results and Phyla by cluster (sarah.bourlat@gmail.com).eml5.5 KB2012-07-25 20:542
To do list for Bioinformatics project.eml3.3 KB2012-07-25 20:542
Regexp explanation.eml4.3 KB2012-07-25 20:543
Re_ Summary-of-Trawl-2-Phyla-by-cluster-csv.csv (c6h5cho@gmail.com).eml8.5 KB2012-07-25 20:541
Re_ may be of use....eml18.8 KB2012-07-25 20:541
Re_ NCBI taxonomy.eml19.5 KB2012-07-25 20:540
MySQL create_modify table.eml1.8 KB2012-07-25 20:541
plos figure.eml48.1 KB2012-07-25 20:540
Joining two SQL queries.eml9.4 KB2012-07-25 20:541
Labbook entry_ Notes on populating the biosql database.eml8.1 KB2012-07-25 20:542
How to query the SQL database.eml1.4 KB2012-07-25 20:542
Here are the revised figures.eml90.4 KB2012-07-25 20:540
Fwd_ Sequence clustering tests before and after removal of ambitious bases.eml66.2 KB2012-07-25 20:542
from blast to sql.eml4.2 KB2012-07-25 20:541
Fwd_ Entering the biosql database.eml29.1 KB2012-07-25 20:541
BLASTX command-line 1.eml44.8 KB2012-07-25 20:541
BLASTX command-line .eml44.8 KB2012-07-25 20:543
BioSQL design notes.eml8.5 KB2012-07-25 20:544
BioSQL database update.eml8.7 KB2012-07-25 20:541
BioSQL database commands.eml18.9 KB2012-07-25 20:541
Biosql database design.eml13.3 KB2012-07-25 20:544
bioseqdb query.eml2.7 KB2012-07-25 20:541
Bioinformatics project update 29.01.2012.eml7.4 KB2012-07-25 20:542
2012-01-160.8 KB2012-07-25 20:546
2012-01-191.6 KB2012-07-25 20:541
2012-01-060.8 KB2012-07-25 20:543
2012-01-101.6 KB2012-07-25 20:543
2012-01-052.0 KB2012-07-25 20:543
2011-12-14 projectoutline.pdf64.8 KB2012-07-25 20:5417
2.eml4.2 KB2012-07-25 20:545
1.eml2.6 KB2012-07-25 20:540
bash_0501127.7 KB2012-07-23 05:131
bash_06011228.8 KB2012-07-23 05:132
bash_060112.21.9 KB2012-07-23 05:132
bash_09011216.0 KB2012-07-23 05:133
bash_090112.225.8 KB2012-07-23 05:133
bash_15121110.3 KB2012-07-23 05:130
bash_151211.2119.8 KB2012-07-23 05:130
bash_10011219.3 KB2012-07-23 05:130
bash_100112.225.5 KB2012-07-23 05:130
bash_14011215.0 KB2012-07-23 05:130
bash_30011218.6 KB2012-07-23 05:131
bash_31011227.2 KB2012-07-23 05:136
bash_01021246.7 KB2012-07-23 05:131
bash_02021265.3 KB2012-07-23 05:131
bash_0802121.2 MB2012-07-23 05:131
bash_100212108.8 KB2012-07-23 05:131
bash_170212156.6 KB2012-07-23 05:132
bash_170212.2223.2 KB2012-07-23 05:131
bash_170212.3116.7 KB2012-07-23 05:133
bash_18021237.9 KB2012-07-23 05:132
bash_240212450.8 KB2012-07-23 05:134
bash_13061253.7 KB2012-07-23 05:131
bash_270212781.6 KB2012-07-23 05:132
201201221.8 KB2012-07-23 04:532
201202014.0 KB2012-07-23 04:531
201201191.1 KB2012-07-23 04:531
20120118.21.8 KB2012-07-23 04:533
201201142.2 KB2012-07-23 04:532
2012011817.6 KB2012-07-23 04:530
201201101.6 KB2012-07-23 04:530
201201060.8 KB2012-07-23 04:531
20120106.20.5 KB2012-07-23 04:531
201201052.0 KB2012-07-23 04:530
Paper
Virkki_Bourlat_Figure_1.pdf88.6 KB2012-07-25 20:2112
Virkki_Bourlat_Figure_2.pdf43.1 KB2012-07-25 20:2120
Virkki_Bourlat_Figure_S1.pdf48.9 KB2012-07-25 20:2118
Virkki_Bourlat_Figure_3.pdf108.0 KB2012-07-25 20:2119
Virkki_Bourlat_Figure_S2.pdf26.7 KB2012-07-25 20:2112
Virkki_Bourlat_Figure_4.pdf70.9 KB2012-07-25 20:2124
Virkki_Bourlat_paper.pages226.2 KB2012-07-25 20:214
Python code
clusters_SQL.py1.0 KB2012-07-25 20:116
filtering.py2.3 KB2012-07-25 20:114
findprimer.py4.6 KB2012-07-25 20:111
loadbioSQL_biosequence.py0.8 KB2012-07-25 20:111
regex6.py1.1 KB2012-07-25 20:110
blastresults_SQL.py0.8 KB2012-07-25 20:111
blastevalue_SQL.py1.1 KB2012-07-25 20:114
Blast.py0.5 KB2012-07-25 20:112
abitofasta2.py1.1 KB2012-07-25 20:110
Test files
testfile3_filtering.fa0.5 KB2012-07-23 23:120
testfile1_findprimer.fa0.4 KB2012-07-23 23:125
testfile2_filtering.txt23 B2012-07-23 23:126
testfile1_filtering.fa0.4 KB2012-07-23 23:120
Results
View of Trawl 2 Blast results and Phyla by cluster.csv8.6 KB2012-07-23 04:391
View-of-Trawl-2-Blast-results-and-Phyla-by-cluster-csv.csv1.1 KB2012-07-23 04:396
Trawl-4-Blast-results-and-Phyla-by-cluster-csv.csv1.0 KB2012-07-23 04:397
Trawl 2 Blast results and Phyla by cluster.csv16.5 KB2012-07-23 04:394
Trawl 4 Blast results and Phyla by cluster.csv5.5 KB2012-07-23 04:393
table 27.6 KB2012-07-23 04:390
Blast_results_by_cluster30.2 KB2012-07-23 04:390
table 121.8 KB2012-07-23 04:392
Blast_results1.6 MB2012-07-23 04:393
blast_result_csv39.9 KB2012-07-23 04:391
blast_result_parsed34.6 KB2012-07-23 04:391
4clustered.uc2.4 KB2012-07-23 04:394
2clustered.uc3.5 KB2012-07-23 04:392
Data
Trawl 4
T4_216_COI_C07.ab1295.1 KB2012-07-22 16:021
T4_213_COI_H12.ab1290.4 KB2012-07-22 16:021
T4_214_COI_A07.ab1291.0 KB2012-07-22 16:021
T4_215_COI_B07.ab1290.9 KB2012-07-22 16:025
T4_210_COI_E12.ab1165.1 KB2012-07-22 16:023
T4_211_COI_F12.ab1290.9 KB2012-07-22 16:021
T4_212_COI_G12.ab1165.1 KB2012-07-22 16:023
T4_208_COI_C12.ab1290.8 KB2012-07-22 16:013
T4_209_COI_D12.ab1290.5 KB2012-07-22 16:011
T4_205_COI_H11.ab1290.3 KB2012-07-22 16:016
T4_206_COI_A12.ab1290.8 KB2012-07-22 16:015
T4_207_COI_B12.ab1290.4 KB2012-07-22 16:014
T4_203_COI_H12.ab1290.4 KB2012-07-22 16:011
T4_204_COI_G11.ab1290.6 KB2012-07-22 16:014
T4_200_COI_E12.ab1290.5 KB2012-07-22 16:011
T4_201_COI_F12.ab1290.6 KB2012-07-22 16:016
T4_202_COI_G12.ab1290.7 KB2012-07-22 16:012
T4_198_COI_C12.ab1290.3 KB2012-07-22 16:012
T4_199_COI_D12.ab1290.3 KB2012-07-22 16:010
T4_196_COI_A12.ab1290.3 KB2012-07-22 16:011
T4_197_COI_B12.ab1290.2 KB2012-07-22 16:014
T4_194_COI_G11.ab1290.6 KB2012-07-22 16:011
T4_195_COI_H11.ab1290.5 KB2012-07-22 16:011
T4_191_COI_D11.ab1290.8 KB2012-07-22 16:012
T4_192_COI_E11.ab1290.8 KB2012-07-22 16:011
T4_193_COI_F11.ab1290.3 KB2012-07-22 16:011
T4_189_COI_B11.ab1290.3 KB2012-07-22 16:015
T4_190_COI_C11.ab1290.3 KB2012-07-22 16:012
T4_187_COI_H10.ab1290.0 KB2012-07-22 16:011
T4_188_COI_A11.ab1290.3 KB2012-07-22 16:015
T4_184_COI_E10.ab1290.4 KB2012-07-22 16:012
T4_185_COI_F10.ab1290.6 KB2012-07-22 16:011
T4_186_COI_G10.ab1290.6 KB2012-07-22 16:012
T4_182_COI_C10.ab1290.5 KB2012-07-22 16:011
T4_183_COI_D10.ab1290.4 KB2012-07-22 16:011
T4_180_COI_G12.ab1285.2 KB2012-07-22 16:001
T4_181_COI_H12.ab1290.2 KB2012-07-22 16:001
T4_177_COI_D12.ab1291.3 KB2012-07-22 16:004
T4_178_COI_E12.ab1291.5 KB2012-07-22 16:001
T4_179_COI_F12.ab1288.9 KB2012-07-22 16:005
T4_175_COI_B12.ab1294.6 KB2012-07-22 16:001
T4_176_COI_C12.ab1289.5 KB2012-07-22 16:001
T4_172_COI_G11.ab1175.2 KB2012-07-22 16:004
T4_173_COI_H11.ab1291.4 KB2012-07-22 16:003
T4_174_COI_A12.ab1290.3 KB2012-07-22 16:001
T4_170_COI_G12.ab1290.9 KB2012-07-22 16:001
T4_171_COI_H12.ab1290.9 KB2012-07-22 16:005
T4_168_COI_E12.ab1290.9 KB2012-07-22 16:002
T4_169_COI_F12.ab1291.0 KB2012-07-22 16:002
T4_165_COI_B12.ab1291.1 KB2012-07-22 16:003
T4_166_COI_C12.ab1290.9 KB2012-07-22 16:002
T4_167_COI_D12.ab1290.9 KB2012-07-22 16:002
T4_163_COI_H11.ab1291.0 KB2012-07-22 16:001
T4_164_COI_A12.ab1291.1 KB2012-07-22 16:001
T4_160_COI_E11.ab1291.0 KB2012-07-22 16:002
T4_161_COI_F11.ab1290.7 KB2012-07-22 16:005
T4_162_COI_G11.ab1291.0 KB2012-07-22 16:001
T4_158_COI_C11.ab1295.0 KB2012-07-22 16:003
T4_159_COI_D11.ab1291.3 KB2012-07-22 16:001
T4_156_COI_A11.ab1291.2 KB2012-07-22 16:002
T4_157_COI_B11.ab1295.0 KB2012-07-22 16:001
T4_154_COI_G10.ab1291.1 KB2012-07-22 16:001
T4_155_COI_H10.ab1291.0 KB2012-07-22 16:001
T4_151_COI_D10.ab1290.9 KB2012-07-22 15:593
T4_152_COI_E10.ab1290.9 KB2012-07-22 15:594
T4_153_COI_F10.ab1290.9 KB2012-07-22 15:591
T4_149_COI_B10.ab1290.8 KB2012-07-22 15:591
T4_150_COI_C10.ab1291.1 KB2012-07-22 15:591
T4_147_COI_B06.ab1290.8 KB2012-07-22 15:591
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T4_145_COI_G04.ab1291.4 KB2012-07-22 15:591
T4_146_COI_H04.ab1290.6 KB2012-07-22 15:591
T4_48_COI_H12.ab1257.2 KB2012-07-22 15:591
T4_46_COI_F12.ab1263.1 KB2012-07-22 15:591
T4_47_COI_G12.ab1257.9 KB2012-07-22 15:593
T4_43_COI_C12.ab1258.7 KB2012-07-22 15:591
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T4_35_COI_C11.ab1266.3 KB2012-07-22 15:592
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T4_33_COI_A11.ab1262.1 KB2012-07-22 15:591
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T4_30_COI_F10.ab1260.8 KB2012-07-22 15:591
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T4_32_COI_H10.ab1260.1 KB2012-07-22 15:592
T4_28_COI_D10.ab1260.3 KB2012-07-22 15:591
T4_29_COI_E10.ab1260.3 KB2012-07-22 15:591
T4_25_COI_A10.ab1263.8 KB2012-07-22 15:581
T4_26_COI_B10.ab1195.8 KB2012-07-22 15:582
T4_27_COI_C10.ab1261.7 KB2012-07-22 15:581
T4_22_COI_F09.ab1260.9 KB2012-07-22 15:585
T4_23_COI_G09.ab1261.8 KB2012-07-22 15:582
T4_24_COI_H09.ab1264.4 KB2012-07-22 15:582
T4_20_COI_D09.ab1261.8 KB2012-07-22 15:581
T4_21_COI_E09.ab1265.1 KB2012-07-22 15:582
T4_17_COI_A09.ab1262.2 KB2012-07-22 15:581
T4_18_COI_B09.ab1267.8 KB2012-07-22 15:581
T4_19_COI_C09.ab1262.9 KB2012-07-22 15:581
T4_15_COI_G08.ab1290.5 KB2012-07-22 15:583
T4_16_COI_H08.ab1175.1 KB2012-07-22 15:584
T4_13_COI_E08.ab1290.7 KB2012-07-22 15:580
T4_14_COI_F08.ab1290.6 KB2012-07-22 15:582
Trawl 2
Trawl2_73_CO1_F12.ab1239.2 KB2012-07-22 15:564
Trawl2_74_CO1_G12.ab1219.1 KB2012-07-22 15:561
Trawl2_75_CO1_H12.ab1238.1 KB2012-07-22 15:564
Trawl2_70_CO1_C12.ab1241.8 KB2012-07-22 15:553
Trawl2_71_CO1_D12.ab1239.3 KB2012-07-22 15:551
Trawl2_72_CO1_E12.ab1239.2 KB2012-07-22 15:551
Trawl2_67_CO1_H11.ab1240.2 KB2012-07-22 15:553
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Trawl2_69_CO1_B12.ab1239.9 KB2012-07-22 15:554
Trawl2_64_CO1_E11.ab1240.9 KB2012-07-22 15:552
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Trawl2_50_CO1_G09.ab1240.1 KB2012-07-22 15:551
Trawl2_51_CO1_H09.ab1241.5 KB2012-07-22 15:551
Trawl2_52_CO1_A10.ab1240.8 KB2012-07-22 15:553
T2_144_COI_G12.ab1291.2 KB2012-07-22 15:551
Trawl2_49_CO1_F09.ab1241.5 KB2012-07-22 15:550
T2_141_COI_H07.ab1295.0 KB2012-07-22 15:555
T2_142_COI_E12.ab1291.0 KB2012-07-22 15:552
T2_143_COI_F12.ab1290.6 KB2012-07-22 15:551
T2_139_COI_F07.ab1290.9 KB2012-07-22 15:550
T2_140_COI_G07.ab1290.6 KB2012-07-22 15:551