Sunday: A Swarm of Cave Pools

Image

I like this sketch I did. This shows the spatial relationship between several cave pools in cross section to the geologic structures in the area. The numbers with the arrows are the strikes of the flowstone and rimstone dams.

The circle in the lower right is an equal hemisphere projection. The lines are best thought of as planes sitting inside a hollow hemisphere. This is one way to represent different geologic features as planes.

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Optimizing PCR reactions for gene amplification Part II

Here is a slightly modified one for those troublesome genes that won’t amplify or if you get lots of smearing.

Basic Master Mix recipe for AmpliTAQ gold

for 15 µL reaction

(volumes in µL)
H2O 9.57
10x PCR Buffer 1.5
100x BSA 0.125
Forward Primer 0.1
Reverse Primer 0.1
TAQ 0.15
MgCl2 1.5
DMSO 1.5

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Trees! and some field work

I’ve been working on this thing here

This shows the effect of different alignment programs on the same 16S data set.
Pretty neat.

I am going out on Saturday to the Ojito Wilderness area to do a strat section on a mesa. I want to show folks what a geosciences notebook looks like.

Sunday will be some data from Lechuguilla Cave (one of the places I work in)

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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

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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.

 

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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

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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.

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