Posting!!!

I can’t remember where I saw this but I need to get in the habit of posting on a regular schedule. Google+ distracts me a lot from posting.

One feature I am going to add is a Sunday post. This will be where I show some of my older work (some complete others in various stages).

Tu/Th – regular posts

Sunday – Past work and field notes

Posted in Uncategorized | Leave a comment

Fieldwork!!!!

Saturday is a fieldwork day. I’ll be posting a bunch of stuff up ranging from notebook scans, GIS files, and maps. All will be CCBY and I will attached the license.

Site: White Mesa

Geologic Overview

I am in the process of redrafting the geologic map for the area. Here is a sneak peak:

Image

The goals for Saturday are:

Locate the active seeps on the spring mounds, locate paleo-springs, trace pressure ridges, and plate some bacteria.

All the data will go into a GIS map (using QGIS). I’ll put the maps and GIS files up here. Hopefully I’ll get some 454 data from my samples up here as well.

 

Posted in Uncategorized | Tagged , , | Leave a comment

Code for your geomicrobiology!!!

Finally a post about geomicrobiology.

Over on github I set up a repo. Most the codes are not comment and there are no docs as of yet.

 

One that might interest geomicro folks is some code I wrote that parses a genbank file for accession number, location, source of sample, and sequence. I combine this into a fasta for that can then be turned into a tree for doing some biogeography or geomicrobiology. You will need to align your fasta and build the tree.

 

Code is HERE

Posted in Uncategorized | Tagged , , , , | Leave a comment

Reference Sequences (NCBI)

In my obsession to create a genus level tree I stumbled across the NCBI RefSeq. This is a high quality 16S dataset from NCBI.

You can access it from an FTP site or at the search bar.

From the NCBI search bar grab the pull down menu and select nucleotide. In the search bar enter the following.

33175[BioProject]

You will get ~7000+ sequences.

I downloaded the whole set. First change the fasta headers to a genus only header:

>Some_genus

Then I wrote this code in python (requires BioPython)

from Bio import SeqIO

def genus_level(fasta_file):

sequences={}
for seq_record in SeqIO.parse(fasta_file, “fasta”):
sequence=seq_record.id
if sequence not in sequences:
sequences[sequence]=str(seq_record.seq)

output_file=open(“clear_”+fasta_file,”w+”)
out_genera=open(“genera_list”+fasta_file,”w+”)

for sequence in sequences:
output_file.write(“>”+sequence+”\n”+sequences[sequence]+”\n”)
out_genera.write(sequence+”\n”)
output_file.close()
out_genera.close()

#Call the f(x) like this:
#genus_level(“my_fasta.fasta”)

Run that on the fasta and BOOM!!!! Genus level fasta file of the RefSeq database. I will get the code cleaned up in the next day or so. I will add in the renaming the fasta header and some filtering options (like scanning for short sequences and so on).

FYI if you notice one of the files kicked out is just a list of genera for you to play with.

Posted in Uncategorized | Tagged , , , | Leave a comment

Network Analysis of the Cyano Tree

Here is the network analysis of the cyano tree. This 16S alignment was done in muscle. The tree was built using PhyML with 100 bootstraps.

The network analysis was carried out in SplitsTree.

Posted in Uncategorized | Tagged , , | Leave a comment

Cyano ML tree

Here is the ML tree for the cyano bacteria by genera with two removed due to bad 16S data.

Image

Posted in Uncategorized | Tagged , , , , | Leave a comment

More trees for your viewing dismay

A few days ago I posted a NJ 1000 bootstrapped cyanobacteria tree at the genera level. Here are a couple of other ways to look at the same data set.

Image

This is an AML tree. You can see some things are in different places.
The big difference I noticed was the placement of the candidatus genera.

Both the NJ and AML tree are different from the NCBI taxonomic structure.

I’ll post the PhyML tree later today.

I am going to remove the short sequences from the cyano tree, run a new alignment, and then compare the trees again.

The newick file for this tree is here:

((((((Limnococcus:0.0543055396,Johannesbaptistia:0.0827145140)70:0.0344450208,Chondrocystis:0.0729476463)53:0.0279920338,(((Solentia:0.0565478859,Hyella:0.0558046996)59:0.0149440458,(Myxosarcina:0.0143627100,((Dermocarpa:0.0090838586,Stanieria:0.0298887512)100:0.0319212685,((Xenococcus:0.0306654901,Pleurocapsa:0.0529666329)97:0.0263862958,Dermocarpella:0.0307601085)84:0.0165593063)59:0.0083008678)100:0.0624117043)43:0.0393172329,(((((((((((Trichocoleus:0.0845592526,Chroogloeocystis:0.0594235144)52:0.0263768491,(Chroococcus:0.0880145666,Chroococcidiopsis:0.1275603493)56:0.0223390003)15:0.0163417632,(Microchaete:3.2941937902,(((((Crinalium:0.0008802610,Starria:0.0725556714)99:0.0769356244,Chamaesiphon:0.1220433027)42:0.0266538083,(((((((Cylindrospermum:0.0430895087,((((((Coleodesmium:0.0019855000,Rexia:0.0185910119)90:0.0149691424,Hassallia:0.0179228155)77:0.0124770313,(Pseudoscytonema:0.0305139345,Uncultured_Richelia:0.0649750928)59:0.0267823784)63:0.0169522963,Spirirestis:0.0399104672)46:0.0345921707,(Mojavia:0.0502289833,Tolypothrix:0.0047592151)72:0.0131213010)17:0.0077281451,((((Calothrix:0.0085082496,Anabaena:0.0897209192)55:0.0151979445,Camptylonemopsis:0.0178761361)58:0.0173368772,(Trichormus:0.0409631812,Anabaenopsis:0.0308688459)98:0.0507930721)25:0.0087945825,(Fortiea:0.0599328005,Nostoc:0.0318855257)18:0.0076194233)8:0.0135365193)2:0.0092326146)4:0.0038240170,(((Raphidiopsis:0.0084712314,Cylindrospermopsis:0.0067275585)100:0.0350623875,Sphaerospermopsis:0.0266622460)98:0.0342990146,Wollea:0.0392845032)99:0.0480554525)0:0.0082196991,((((Cyanospira:0.0272434458,Nodularia:0.0303054134)74:0.0166932171,Umezakia:0.0358745909)66:0.0096985007,((Dolichospermum:0.0013565773,Aphanizomenon:0.0063531148)100:0.0390046417,Cuspidothrix:0.0490716892)97:0.0307378581)16:0.0039297611,Gloeotrichia:0.1261188474)12:0.0121215958)15:0.0179228257,(Stigonema:0.0438563149,(Petalonema:0.0339177052,Capsosira:0.0581682710)44:0.0240729296)16:0.0197428491)32:0.0171179575,(((((Westiellopsis:0.0152923821,Hapalosiphon:0.0290265101)71:0.0204530495,Nostochopsis:0.0192930816)100:0.0375972724,(Mastigocladus:0.0011028859,Fischerella:0.0026556062)100:0.0888819220)78:0.0265307267,Chlorogloeopsis:0.1031979664)63:0.0138862847,Rivularia:0.1015247325)32:0.0126707007)16:0.0086900666,Scytonematopsis:0.1270558400)37:0.0082529310,((Brasilonema:0.0375396638,((Iphinoe:0.0114128798,Symphyonemopsis:0.0159845680)100:0.0319429392,Scytonema:0.1118834077)35:0.0082325641)50:0.0200321933,(Mastigocladopsis:0.0363274273,Symphyonema:0.0514882467)72:0.0255197169)72:0.0216286012)68:0.0382440977)6:0.0223698398,(Wilmottia:0.0280695032,Hormoscilla:0.0194230275)100:0.0806008070)1:0.0012637447,(Loriellopsis:0.0916794075,Plectonema:0.1246701722)29:0.0364987647)1:0.0065504130)0:0.0000213631)1:0.0231823214,Pseudanabaena:0.1656468029)0:0.0048665047,((Methanocaldococcus:4.5620715748,Symploca:0.0499612094)1:0.0000242825,(Moorea:0.0424026717,Schizothrix:0.0603348702)93:0.0454078928)1:0.0337228245)0:0.0086556421,((Oscillatoria:0.0180910320,Phormidium:0.0038345668)100:0.1083669419,(Planktothricoides:0.1474494446,((Desertifilum:0.1231389559,Pseudoscillatoria:0.1172493477)64:0.0608279908,(((Tychonema:0.0247008096,Microcoleus:0.0255393621)100:0.0621785623,(((Symplocastrum:0.0017341035,Blennothrix:0.0127629204)71:0.0118772978,Hydrocoleum:0.0464332764)44:0.0101616270,Trichodesmium:0.0262792138)100:0.0738871439)44:0.0112265496,(((Arthrospira:0.0036035480,Spirulina:0.0034321365)100:0.0496378848,Lyngbya:0.0520722943)89:0.0254526616,Planktothrix:0.1574632224)17:0.0182371747)18:0.0106061863)1:0.0027617597)0:0.0064997552)2:0.0203181605)0:0.0149033793,((((Planktolyngbya:0.0649382523,Limnothrix:0.1970967400)30:0.0523259811,((Tapinothrix:0.1083835743,Plectolyngbya:0.0848674559)79:0.0494241348,Romeria:0.1394751273)54:0.0449033338)10:0.0332090681,Arthronema:0.0882816659)8:0.0416833591,((((Thermosynechococcus:0.0177456642,Synechococcus:0.0048970458)100:0.0936297297,Aphanocapsa:0.0431221365)65:0.0265767257,Acaryochloris:0.1130397694)30:0.0215642832,(((((Halomicronema:0.0859311198,(Nodosilinea:0.0527282792,Haloleptolyngbya:0.0692337431)99:0.0491872765)24:0.0181959139,(Leptolyngbya:0.1061522162,Pseudophormidium:0.0861900283)42:0.0285976662)21:0.0218354835,Prochlorothrix:0.1039802682)19:0.0075813211,(Jaaginema:0.1439699514,(Merismopedia:0.0194576660,((Prochlorococcus:0.0667450851,Cyanodictyon:0.0030830827)52:0.0063483954,Cyanobium:0.0096935315)59:0.0087606677)92:0.1194728238)17:0.0366526652)11:0.0203338112,(Gloeobacter:0.1642330110,Chlorogloea:0.1038778876)25:0.0605400448)6:0.0359408989)1:0.0099348650)0:0.0244375123)2:0.0317513322,Prochloron:0.1034279892)1:0.0075801850,((Chroococcopsis:0.0949580129,Cyanobacterium:0.0787609893)96:0.1207597758,(((Halospirulina:0.0559544587,Aulosira:0.1579393772)85:0.0616160327,Geitlerinema:0.1273880648)15:0.0169191192,((Dactylococcopsis:0.0459940135,Cyanothece:0.0350513305)100:0.0950093180,(Rubidibacter:0.0958104807,Halothece:0.1030371781)81:0.0446507128)49:0.0236324398)33:0.0219272790)5:0.0116565596)1:0.0094555589,(Rhabdoderma:0.1119214060,(((Radiocystis:0.0931314877,Gloeothece:0.0579325054)58:0.0190687488,Microcystis:0.1026691837)53:0.0179869029,((Woronichinia:0.0393573655,Snowella:0.0676299563)98:0.0367508722,Synechocystis:0.0479859932)91:0.0365259331)78:0.0205312028)5:0.0136663395)0:0.0071853366,Komvophoron:0.1378140913)0:0.0049130416)0:0.0105862343)0:0.0239406424,Aphanothece:0.0553651193)1:0.0586166557,(Gloeocapsa:0.0217367744,Crocosphaera:0.0161067250)90:0.0000065241)27:0.1966092526,Cyanosarcina:0.1393880769,Gloeocapsopsis:2.5790516588);

Posted in Uncategorized | Tagged , , , , , | 7 Comments