Hi Chris, Attached is the KO data, base media and WT data (without CAS amino acids, with no replicates, and with Phosphate added to the missing media definitions). You are also correct that there are many replicates in there. I thought we wanted to keep them in there to compare the KO results more easily. I took them out. Ben ----------------------------- Email: [email protected] Phone: (510) 214-6683 MS 977-221, Lawrence Berkeley Lab Web: ms.lbl.gov On Thu, Feb 14, 2013 at 11:37 AM, Paramvir Dehal <[email protected]> wrote:
Hey Chris,
I'll take care of the BLAST'ing
Paramvir
On Thu, Feb 14, 2013 at 9:37 AM, Christopher Henry <[email protected]> wrote:
Hi all,
So I have a couple of really URGENT requests for data and help I need with the Adam D. demo.
1.) I need a list of ALL paralogs in the g.20848 genome (related to mutant phenotype analysis) -Please blast all g.20848 genes against the g.20848 genome and provide me with a list of all hits -The list should have two columns: gene ID and blast score (and other blast metrics)
2.) I need a list of ALL hits between genes in the g.20848 genome and genomes in KBase (related to mutant phenotype analysis) -Provide me with a four column list: gene ID in g.20848, gene ID of hit in other genome, annotation of gene we hit, blast score, maybe other blast metrics
3.) MOST URGENT: I had issues with the wild type conditions Ben sent (related to IMMEDIATE phenotype analysis) -you gave me 100 conditions, but there were many repeated conditions (any idea why???) -You gave me some conditions that had no phosphate source at all
I translated your wild type conditions into 60 media formulations (listed below). In the list below, the name of the media is in the first column, and the full list of compounds is in the second column. The prefix in the media name reflects my understanding of the study: "C-" means a study of carbon source "N-" means a study of nitrogen source "CN-" means a single compound serving as carbon and nitrogen source "P-" means phosphate source "S-" means sulfate source
Note, I actually had to change three of your conditions because there was no phosphate source at all. But now I'm uncertain how these correspond to your knockout phenotypes. Can you resend me the knockout phenotype data specified in terms of my media names below? And can you send it today (ASAP)? If I have it by tonight, everything will be done tomorrow.
Chris
P.S. I understand (well… really really hope!) there are services in KBase to get me (1) and (2), and I'd love to hear about them. HOWEVER, please also run the commands yourself and send me the requested data directly… I need to try and shave time wherever possible.
P.P.S. All work is being conducted in workspace "phenotypeDemo"
C-Butyrate Butyrate;NH4+;Phosphate;Sulfate;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ C-Cytidine Cytidine;NH4+;Phosphate;Sulfate;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ C-Lactate D-Lactate;L-Lactate;NH4+;Phosphate;Sulfate;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ C-D-Lactate D-Lactate;NH4+;Phosphate;Sulfate;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ C-Guanosine Guanosine;NH4+;Phosphate;Sulfate;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ C-Inosine Inosine;NH4+;Phosphate;Sulfate;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ C-L-glutamate L-glutamic acid;NH4+;Phosphate;Sulfate;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ C-L-glutamine L-glutamine;NH4+;Phosphate;Sulfate;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ C-L-isoleucine L-isoleucine;NH4+;Phosphate;Sulfate;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ C-L-lactate L-lactate;NH4+;Phosphate;Sulfate;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ C-L-leucine L-leucine;NH4+;Phosphate;Sulfate;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ C-L-serine L-serine;NH4+;Phosphate;Sulfate;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ C-N-acetyl-D-glucosamine N-acetyl-D-glucosamine;NH4+;Phosphate;Sulfate;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ C-acetate NH4+;Phosphate;Sulfate;acetate;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ C-adenosine NH4+;Phosphate;Sulfate;adenosine;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ C-alpha-ketoglutarate NH4+;Phosphate;Sulfate;alpha ketoglutaric acid;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ C-gly-asp-L NH4+;Phosphate;Sulfate;gly-asp-L;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ C-gly-glu-L NH4+;Phosphate;Sulfate;gly-glu-L;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ C-malate NH4+;Phosphate;Sulfate;malic acid;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ C-propionate NH4+;Phosphate;Sulfate;propionate;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ C-pyruvate NH4+;Phosphate;Sulfate;pyruvate;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ C-Uridine NH4+;Phosphate;Sulfate;Uridine;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ CN-Cytidine Cytidine;Phosphate;Sulfate;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ CN-L-glutamate L-glutamic acid;Phosphate;Sulfate;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ CN-L-glutamine L-glutamine;Phosphate;Sulfate;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ CN-L-isoleucine L-isoleucine;Phosphate;Sulfate;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ CN-L-serine L-serine;Phosphate;Sulfate;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ CN-L-threonine L-threonine;Phosphate;Sulfate;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ CN-Aspartate Aspartic acid;D-Lactate;L-Lactate;Phosphate;Sulfate;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ CN-L-Arginine D-Lactate;L-Arginine;L-Lactate;Phosphate;Sulfate;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ CN-L-Asparagine D-Lactate;L-Asparagine;L-Lactate;Phosphate;Sulfate;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ CN-L-Glycine D-Lactate;L-Glycine;L-Lactate;Phosphate;Sulfate;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ CN-L-Histidine D-Lactate;L-Histidine;L-Lactate;Phosphate;Sulfate;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ CN-L-alanine D-Lactate;L-Lactate;L-alanine;Phosphate;Sulfate;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ CN-L-asparagine D-Lactate;L-Lactate;L-asparagine;Phosphate;Sulfate;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ CN-L-glutamate D-Lactate;L-Lactate;L-glutamic acid;Phosphate;Sulfate;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ CN-L-glutamine D-Lactate;L-Lactate;L-glutamine;Phosphate;Sulfate;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ CN-L-glycine D-Lactate;L-Lactate;L-glycine;Phosphate;Sulfate;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ CN-L-isoleucine D-Lactate;L-Lactate;L-isoleucine;Phosphate;Sulfate;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ CN-L-leucine D-Lactate;L-Lactate;L-leucine;Phosphate;Sulfate;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ CN-L-methionine D-Lactate;L-Lactate;L-methionine;Phosphate;Sulfate;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ CN-L-phenylalanine D-Lactate;L-Lactate;L-phenylalanine;Phosphate;Sulfate;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ CN-L-proline D-Lactate;L-Lactate;L-proline;Phosphate;Sulfate;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ CN-L-serine D-Lactate;L-Lactate;L-serine;Phosphate;Sulfate;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ CN-L-threonine D-Lactate;L-Lactate;L-threonine;Phosphate;Sulfate;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ CN-N-acetyl-D-glucosamine D-Lactate;L-Lactate;N-acetyl-D-glucosamine;Phosphate;Sulfate;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ CN-Adenosine D-Lactate;L-Lactate;Phosphate;Sulfate;adenosine;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ CN-Putrescine D-Lactate;L-Lactate;Phosphate;Sulfate;putrescine;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ CN-N-acetyl-D-glucosamine N-acetyl-D-glucosamine;Phosphate;Sulfate;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ P-Cytidine-5-monophosphate D-Lactate;L-Lactate;NH4+;Sulfate;cytidine 5' monophosphate;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ P-Glycerol-3-phosphate D-Lactate;L-Lactate;NH4+;Sulfate;glycerol 3-phosphate;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ P-O-phosphoryl-ethanolamine D-Lactate;L-Lactate;NH4+;Sulfate;o-phosphoryl-ethanolamine;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ P-Tripolyphosphate D-Lactate;L-Lactate;NH4+;Sulfate;tripolyphosphate;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ S-Cysteine Cysteine;D-Lactate;L-Lactate;NH4+;Phosphate;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ S-Glutathione D-Lactate;L-Lactate;NH4+;glutathione;Phosphate;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ S-Hypotaurine D-Lactate;L-Lactate;NH4+;hypotaurine;Phosphate;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ S-Sulfate D-Lactate;L-Lactate;NH4+;Sulfate;Phosphate;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ S-Sulfite D-Lactate;L-Lactate;NH4+;sulfite;Phosphate;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ S-Thiosulfate D-Lactate;L-Lactate;NH4+;thiosulfate;Phosphate;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ S-Thiourea D-Lactate;L-Lactate;NH4+;thiourea;Phosphate;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+
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