Dr. Rasmus Nielsen Laboratory - Revision history

Christoph at 15:39, 5 July 2012

2012-07-05T15:39:24Z

Christoph at 00:53, 26 July 2006

2006-07-26T00:53:47Z

Christoph at 00:48, 26 July 2006

2006-07-26T00:48:33Z

Show changes

Christoph at 02:14, 23 July 2006

2006-07-23T02:14:44Z

Christoph: format

2006-05-31T20:51:18Z

format

Christoph: /* Overview of research */ Added "batch execution example"

2006-01-26T16:30:22Z

‎Overview of research: Added "batch execution example"

Christoph: /* Overview of research */ "Blastall" link

2006-01-23T23:24:02Z

‎Overview of research: "Blastall" link

Christoph: /* Overview of research */ Added "BLAST" section

2006-01-23T22:33:09Z

‎Overview of research: Added "BLAST" section

Christoph: /* Data */ format

2006-01-14T21:58:17Z

‎Data: format

Christoph: /* trnL */ temp link to "glauca"

2006-01-12T21:51:51Z

‎trnL: temp link to "glauca"

← Older revision		Revision as of 15:39, 5 July 2012
Line 1:		Line 1:
−	The '''[http://www.binf.ku.dk/~rasmus/webpage/ras.html Dr. Rasmus Nielsen Laboratory]''' is where I did research from December 2005-February 2006). It is located at the ''[http://www.binf.ku.dk/~~view/Main~~ Centre for Bioinformatics]'', [http://www.ku.dk/ København Universitet], Denmark.	+	The '''[http://www.binf.ku.dk/~rasmus/webpage/ras.html Dr. Rasmus Nielsen Laboratory]''' is where I did research from December 2005-February 2006). It is located at the ''[http://www.binf.ku.dk/ Centre for Bioinformatics]'', [http://www.ku.dk/ København Universitet], Denmark.

	== Research topics ==		== Research topics ==

@@ Line 1: / Line 1: @@
 The '''[http://www.binf.ku.dk/~rasmus/webpage/ras.html Dr. Rasmus Nielsen Laboratory]''' is where I did research from December 2005-February 2006). It is located at the ''[http://www.binf.ku.dk/view/Main Centre for Bioinformatics]'', [http://www.ku.dk/ København Universitet], Denmark.
-==Overview of research==
+== Research topics ==
-* '''[[BLAST]]''' (ignore ''E''-value; remove redundancy)
+== External links ==
-** [[FASTA format]]
-** [[Formatdb]]: <tt>formatdb -i databasefile -p F -o -n basename</tt>
-** [[Blastall]]: <tt>blastall -p blastn -d database_to_be_searched -i name_of_input_file -o name_of_output_file</tt>
-* '''Taxonomy''' (from GenBank files)
-* '''[[Clustal]]''' (align top 50 from BLAST output)
-** [[ClustalW]]: <tt>clustalw all.fsa</tt>
-** [[ClustalX]]: <tt>clustalx all.aln</tt>
-** [[NJplot]]: <tt>njplot all.ph</tt>
-* '''[[MrBayes]]'''
-** [[Bayesian inference]]
-** [[Phylogenetics]]
-** [[Bayesian Phylogenetic Analysis]]
-** [[Markov chain Monte Carlo]]
-** [[NEXUS file format]]
-** MrBayes batch execution example:
-<pre>
-set autoclose=yes nowarn=yes
-execute TB554_3C.nex
-lset nst=6 rates=invgamma
-mcmc ngen=1000000 samplefreq=100
-sump burnin=2500
-sumt burnin=2500
-quit
-</pre>
-−
-* '''Find probability of each group'''
-−
-==Test runs==
-−
-* Nucleotide model: '''General Time Reversible''' ('''GTR''') (option: +gamma): <tt>lset nst=2 rates=gamma</tt>
-* ('''Do not do the following!''') Constrain all phylogenetic groups to be monophyletic.
-* Make option: <tt>strict clock trees</tt> (uniform) (<tt>prset brlenspr=clock:uniform</tt>)
-−
-* 1,000,000 updates (e.g. cycles)
-* discard first 50,000 as burn-in
-* sample a total of 10,000 trees (say)
-−
-* Then process output to get probabilities of each possible phylogenetic assignment of query sequence.
-−
-In MrBayes, if you run the program with the constraints of monophyletic groups, you are forcing the query sequence '''not''' to be part of these groups. So that won't work.
-−
-Instead, run it without the constraints and simply check how often the query sequence is member of a partition that only contains one particular phylogenetic group as members (at any phylognetic level, e.g. species, genus, family, order, etc).
-−
-Remember, MrBayes will output the probabililities of specific groups (or partitions) directly. So you don't have to do anything with trees yourself.
-−
-<div style="padding: 1em; margin: 10px; border: 2px dotted blue;">
-<small><font color=blue>1</font></small>Maybe we should use <tt>nst=6</tt>. Maybe also in the initila analyses we should
-not assume a molecular clock, i.e. we should not use the <tt>prset brlenspr=clock:uniform option.l</tt>
-−
-OK, so plateauing around 100,000 means that we should not use the first 100,000 iterations (1000 samples with samplefreq=100). We then want to know often the query sequence is part of a bipartition which, in addition to the the query sequence itself, only contain members of a particular taxonomic group. We want to do that at all taxonomic levels. You use the <tt>sumt burnin=1000</tt> command to get output that specifies all the most supported partitions. For each taxonomic assignment in you database data, you then check how many times the query sequence is a member of at least one partition (one of the two sets defined by an edge in the tree) which except for the query sequence only counts sequences belonging to that taxonomix assignment as its members.
-−
-For example, if you have 8 database sequences and sequence 1, 2, 3 and 5 belong to group 'waggadoodles', and you have the following output:
-<pre>
-...*.***.
-*.......*
-.*......*
-******..*
-..**....*
-</pre>
-−
-where the last sequence is the query sequence, then the probability of the query sequence belonging to the waggadoodles is 60% because it formed a unqiue (monophyletic) group with at least some waggadoodles in 3 out of 5 cases (case 1, 2 and 3).
-</div>
-−
 ==External links==
 ===Taxonomy===
 * [http://plants.usda.gov/ PLANTS Database] &mdash; by the USDA
@@ Line 80: / Line 20: @@
 ===References===
 * [http://workshop.molecularevolution.org/resources/references/ Molecular Evolution papers]
 [[Category:Academic Research]]

← Older revision		Revision as of 02:14, 23 July 2006
Line 1:		Line 1:
−	'''[http://www.binf.ku.dk/~rasmus/webpage/ras.html Dr. Rasmus Nielsen Laboratory]''' is where I did research from December 2005-February 2006). It is located at the ''[http://www.binf.ku.dk/view/Main Centre for Bioinformatics]'', [http://www.ku.dk/ København Universitet], Denmark.	+	The '''[http://www.binf.ku.dk/~rasmus/webpage/ras.html Dr. Rasmus Nielsen Laboratory]''' is where I did research from December 2005-February 2006). It is located at the ''[http://www.binf.ku.dk/view/Main Centre for Bioinformatics]'', [http://www.ku.dk/ København Universitet], Denmark.

	==Overview of research==		==Overview of research==

@@ Line 1: / Line 1: @@
-'''[http://www.binf.ku.dk/~rasmus/webpage/ras.html Dr. Rasmus Nielsen Laboratory]''' is where I am currently doing research (December 2005-present). It is located at the ''[http://www.binf.ku.dk/view/Main Centre for Bioinformatics]'', [http://www.ku.dk/ København Universitet], Denmark.
+'''[http://www.binf.ku.dk/~rasmus/webpage/ras.html Dr. Rasmus Nielsen Laboratory]''' is where I did research from December 2005-February 2006). It is located at the ''[http://www.binf.ku.dk/view/Main Centre for Bioinformatics]'', [http://www.ku.dk/ København Universitet], Denmark.
-−
-==Professor Information==
-* '''Rasmus Nielsen''' (Ole Roemer Fellow)
-* Office: 314
-* Phone: +45 3532 1279
-* E-mail: rasmus@binf.ku.dk
 ==Overview of research==

@@ Line 24: / Line 24: @@
 ** [[Markov chain Monte Carlo]]
 ** [[NEXUS file format]]
 * '''Find probability of each group'''

@@ Line 81: / Line 81: @@
 '''Description''': Here are some sequences from a gene called trnL. For these and all the other sequences, we want the database sequences to be considerably longer, i.e. maybe 500 bp or 1000 bp to the 3' and 5' of our sequences - or however much there typicaly is in the relvant database sequences.<br />
 '''Contains''':<br />
-* Mike_1_4C.fasta
+* '''Mike_1_4C''' (n/a)
 ** >Mike_1_4C
 ** >Araucaria_araucana* AY145322
@@ Line 91: / Line 91: @@
 ** >Larix_occidentalis AF440502
 ** >Larix_potaninii_potaninii AF440495
-* Mike_2_Betulaceae.fasta
+* '''Mike_2_Betulaceae''' (n/a)
 ** >Mike_2_Betulaceae
 ** >Betula_pendula AF327578
@@ Line 103: / Line 103: @@
 ** >Lophostemon_confertus AF190385
 ** >Allosyncarpia_ternata AF190387
-* Mike_3.fasta
+* '''Mike_3''' (n/a)
 ** >Mike_3
 ** >Gaylussacia_brasiliensis AF271713
@@ Line 114: / Line 114: @@
 ** >Bejaria_aestuans AF394264
 ** >Ledum_palustre AF394252
-* Mike_4_2C.fasta
+* '''Mike_4_2C''' (n/a)
 ** >Mike_4_2C
 ** >Taxus_yunnanensis AF501590
@@ Line 122: / Line 122: @@
 ** >Taxus_chinensis_mairei AF501588
 ** >Taxus_canadensis AF506837
-* TB458_478_8C_Poaceae.fasta
+* '''TB458_478_8C_Poaceae''' (1sub)
 ** >TB458_478_8C_Poaceae_1sub
 ** >Poa_pratensis AY061952
@@ Line 134: / Line 134: @@
 ** >Dupontia_fisheri AY237899
 ** >Festuca_paniculata AF543515
-* TB458_478_9C_Rhamnaceae.fasta
+* '''TB458_478_9C_Rhamnaceae''' (4sub)
 ** >TB458_478_9C_Rhamnaceae_4sub
 ** >Paliurus_spina_christi AJ390354
@@ Line 147: / Line 147: @@
 ** >Colubrina_asiatica AJ390350
 ** >Retanilla_stricta AY460425
-* TB487_12_1C_Poaceae.fasta
+* '''TB487_12_1C_Poaceae''' (0sub)
 ** >TB487_12_1C_Poaceae_0sub
 ** >Poa_pratensis AY061951
@@ Line 159: / Line 159: @@
 ** >Dupontia_fisheri AY237899
 ** >Festuca_paniculata AF543515
-* TB487_14_2C_Veroniceae.fasta
+* '''TB487_14_2C_Veroniceae''' (0sub)
 ** >TB487_14_2C_Veroniceae_0sub
 ** >Veronica_sublobata AF486366
@@ Line 171: / Line 171: @@
 ** >Nemesia_aff_denticulata DQ222330
 ** >Nemesia_foetens DQ222328
-* TB487_18_2C_Polygonaceae.fasta
+* '''TB487_18_2C_Polygonaceae''' (0sub)
 ** >TB487_18_2C_Polygonaceae_osub
 ** >Rheum_wittrockii AY566464
@@ Line 185: / Line 185: @@
 ** >Rumex_cristatus AJ704864
 ** >Rumex_japonicus AJ810936
-* TB487_23_1C_Betulaceae.fasta
+* '''TB487_23_1C_Betulaceae''' (0sub)
 ** >TB487_23_1C_Betulaceae_0sub
 ** >Corylus_avellana AY147072
@@ Line 198: / Line 198: @@
 ** >Engelhardia_fenzelii AY147076
 ** >Eucalyptus_viminalis AF306336
-* TB496_8_2C_Saliceae.fasta
+* '''TB496_8_2C_Saliceae''' (0sub)
 ** >TB496_8_2C_Saliceae_0sub
 ** >Salix_sericea AY756930
@@ Line 210: / Line 210: @@
 ** >Populus_nigra AF327591
 ** >Zuelania_guidonia AY756911
-* TB554_19_1C_Rutaceae.fasta
+* '''TB554_19_1C_Rutaceae''' (0sub)
 ** >TB554_19_1C_Rutaceae_0sub
 ** >Hesperethusa_crenulata AY295298
@@ Line 222: / Line 222: @@
 ** >Balsamocitrus_dawei AY295278
 ** >Citrus_paradisi AY295277
-* TB554_22_4C_Brassicaceae.fasta
+* '''TB554_22_4C_Brassicaceae (0sub)
 ** >TB554_22_4C_Brassicaceae_0sub
 ** >Capsella_bursa_pastoris AY236218
@@ Line 234: / Line 234: @@
 ** >Conringia_perfoliata AY722610
 ** >Lepidium_trifurcum AY015900
-* TB554_6_5C_Saliceae.fasta
+* '''TB554_6_5C_Saliceae''' (0sub)
 ** >TB554_6_5C_Saliceae_0sub
 ** >Salix_sericea AY756930

@@ Line 215: / Line 215: @@
 ** >Triphasia_trifolia AY295297
 ** >Afraegle_paniculata AY295295
-** >Eremocitrus_glauca AY295293
+** >Eremocitrus_glauca AY295293 '''<-- [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=76963], [http://www.ars-grin.gov/cgi-bin/npgs/html/taxon.pl?15354]'''
 ** >Severinia_buxifolia AY295290
 ** >Microcitrus_garrowayi AY295287