https://sourceforge.net/p/appbiokth2011/wiki/Taxonomy%2520assignment/Recent changes to Taxonomy assignmentenWed, 25 Jul 2012 06:13:05 -0000https://sourceforge.net/p/appbiokth2011/wiki/Taxonomy%2520assignment/<pre>--- v34 +++ v35 @@ -8,7 +8,7 @@ This is the link to the [python code](https://sourceforge.net/p/appbiokth2011/code/ci/78249081e205a0142525f036bb9fcced0690eb6e/tree/) -Here are links to the documentation, test files python codes written for this project: +Here are links to the documentation, test files, and python codes written for this project: [abitofasta.py] @@ -23,8 +23,6 @@ [loadbioSQL] -This is the link to the [bioSQL database] - [1]:http://www.python.org/ [2]:http://www.ncbi.nlm.nih.gov/genbank/ [3]:http://www.biosql.org/wiki/Main_Page </pre>Sarah BourlatWed, 25 Jul 2012 06:13:05 -0000https://sourceforge.netabd51f9f3ce7dd26e3f931eb96844072bc835fefhttps://sourceforge.net/p/appbiokth2011/wiki/Taxonomy%2520assignment/<pre>--- v33 +++ v34 @@ -1,4 +1,7 @@ -The aim of this project is to create an automated pipeline for the taxonomic assignment of DNA sequences from environmental samples. In this study, we focus on DNA markers amplified from benthic sediment samples. Using a series of customized scripts written in [python][1], DNA sequences were edited as follows: short sequence removal, primer pair removal and reversal to the correct orientation. Clean marker sequences were then clustered in operational taxonomic units (OTUs) and matched up against the [Genbank database][2]. All sequences and associated data were stored in a [biosql relational database][3], which was then queried to retrieve taxonomy assignments for each cluster. This is an illustration of the pipeline (<a href="http://imgur.com/mFh4h"><img src="http://i.imgur.com/mFh4h.png" alt="" title="Hosted by imgur.com" /></a>). +The aim of this project is to create an automated pipeline for the taxonomic assignment of DNA sequences from environmental samples. In this study, we focus on DNA markers amplified from benthic sediment samples. Using a series of customized scripts written in [python][1], DNA sequences were edited as follows: short sequence removal, primer pair removal and reversal to the correct orientation. Clean marker sequences were then clustered in operational taxonomic units (OTUs) and matched up against the [Genbank database][2]. All sequences and associated data were stored in a [biosql relational database][3], which was then queried to retrieve taxonomy assignments for each cluster. Below is an illustration of the pipeline. + + +<a href="http://imgur.com/LhFhd"><img src="http://i.imgur.com/LhFhd.jpg" alt="" title="Hosted by imgur.com" /></a> This is the link to the [project files](https://sourceforge.net/projects/appbiokth2011/files/) containing [data](https://sourceforge.net/projects/appbiokth2011/files/KTH_Project/Data/), [results](https://sourceforge.net/projects/appbiokth2011/files/KTH_Project/Results/), [Sarah's notebook](https://sourceforge.net/projects/appbiokth2011/files/KTH_Project/Sarahs%20notebook/), [Minttu's notebook](https://sourceforge.net/projects/appbiokth2011/files/KTH_Project/Minttus%20notebook/) and [paper](https://sourceforge.net/projects/appbiokth2011/files/KTH_Project/Paper/). </pre>MV2012Tue, 24 Jul 2012 18:03:14 -0000https://sourceforge.net5ee36f233eccdadc076c33f210874a7b085d1e47https://sourceforge.net/p/appbiokth2011/wiki/Taxonomy%2520assignment/<pre>--- v32 +++ v33 @@ -1,4 +1,4 @@ -The aim of this project is to create an automated pipeline for the taxonomic assignment of DNA sequences from environmental samples. In this study, we focus on DNA markers amplified from benthic sediment samples. Using a series of customized scripts written in [python][1], DNA sequences were edited as follows: short sequence removal, primer pair removal and reversal to the correct orientation. Clean marker sequences were then clustered in operational taxonomic units (OTUs) and matched up against the [Genbank database][2]. All sequences and associated data were stored in a [biosql relational database][3], which was then queried to retrieve taxonomy assignments for each cluster. This is an illustration of the pipeline (http://imgur.com/delete/D9PdMZke6qwUThD). +The aim of this project is to create an automated pipeline for the taxonomic assignment of DNA sequences from environmental samples. In this study, we focus on DNA markers amplified from benthic sediment samples. Using a series of customized scripts written in [python][1], DNA sequences were edited as follows: short sequence removal, primer pair removal and reversal to the correct orientation. Clean marker sequences were then clustered in operational taxonomic units (OTUs) and matched up against the [Genbank database][2]. All sequences and associated data were stored in a [biosql relational database][3], which was then queried to retrieve taxonomy assignments for each cluster. This is an illustration of the pipeline (<a href="http://imgur.com/mFh4h"><img src="http://i.imgur.com/mFh4h.png" alt="" title="Hosted by imgur.com" /></a>). This is the link to the [project files](https://sourceforge.net/projects/appbiokth2011/files/) containing [data](https://sourceforge.net/projects/appbiokth2011/files/KTH_Project/Data/), [results](https://sourceforge.net/projects/appbiokth2011/files/KTH_Project/Results/), [Sarah's notebook](https://sourceforge.net/projects/appbiokth2011/files/KTH_Project/Sarahs%20notebook/), [Minttu's notebook](https://sourceforge.net/projects/appbiokth2011/files/KTH_Project/Minttus%20notebook/) and [paper](https://sourceforge.net/projects/appbiokth2011/files/KTH_Project/Paper/). </pre>MV2012Tue, 24 Jul 2012 17:48:15 -0000https://sourceforge.net6836e42db6e126bc0a5762c0383ee4c9d9d275b9https://sourceforge.net/p/appbiokth2011/wiki/Taxonomy%2520assignment/<pre>--- v31 +++ v32 @@ -1,4 +1,4 @@ -The aim of this project is to create an automated pipeline for the taxonomic assignment of DNA sequences from environmental samples. In this study, we focus on DNA markers amplified from benthic sediment samples. Using a series of customized scripts written in [python][1], DNA sequences were edited as follows: short sequence removal, primer pair removal and reversal to the correct orientation. Clean marker sequences were then clustered in operational taxonomic units (OTUs) and matched up against the [Genbank database][2]. All sequences and associated data were stored in a [biosql relational database][3], which was then queried to retrieve taxonomy assignments for each cluster. This is an illustration of the pipeline +The aim of this project is to create an automated pipeline for the taxonomic assignment of DNA sequences from environmental samples. In this study, we focus on DNA markers amplified from benthic sediment samples. Using a series of customized scripts written in [python][1], DNA sequences were edited as follows: short sequence removal, primer pair removal and reversal to the correct orientation. Clean marker sequences were then clustered in operational taxonomic units (OTUs) and matched up against the [Genbank database][2]. All sequences and associated data were stored in a [biosql relational database][3], which was then queried to retrieve taxonomy assignments for each cluster. This is an illustration of the pipeline (http://imgur.com/delete/D9PdMZke6qwUThD). This is the link to the [project files](https://sourceforge.net/projects/appbiokth2011/files/) containing [data](https://sourceforge.net/projects/appbiokth2011/files/KTH_Project/Data/), [results](https://sourceforge.net/projects/appbiokth2011/files/KTH_Project/Results/), [Sarah's notebook](https://sourceforge.net/projects/appbiokth2011/files/KTH_Project/Sarahs%20notebook/), [Minttu's notebook](https://sourceforge.net/projects/appbiokth2011/files/KTH_Project/Minttus%20notebook/) and [paper](https://sourceforge.net/projects/appbiokth2011/files/KTH_Project/Paper/). </pre>MV2012Tue, 24 Jul 2012 17:47:25 -0000https://sourceforge.netf510625c72b4ae2613216b9e84f176501b2e7975https://sourceforge.net/p/appbiokth2011/wiki/Taxonomy%2520assignment/<pre>--- v30 +++ v31 @@ -1,4 +1,4 @@ -The aim of this project is to create an automated pipeline for the taxonomic assignment of DNA sequences from environmental samples. In this study, we focus on DNA markers amplified from benthic sediment samples. Using a series of customized scripts written in [python][1], DNA sequences were edited as follows: short sequence removal, primer pair removal and reversal to the correct orientation. Clean marker sequences were then clustered in operational taxonomic units (OTUs) and matched up against the [Genbank database][2]. All sequences and associated data were stored in a [biosql relational database][3], which was then queried to retrieve taxonomy assignments for each cluster. This is an illustration of the pipeline ![PRoblem] (https://sourceforge.net/p/appbiokth2011/wiki/Taxonomy%20assignment/#489f) +The aim of this project is to create an automated pipeline for the taxonomic assignment of DNA sequences from environmental samples. In this study, we focus on DNA markers amplified from benthic sediment samples. Using a series of customized scripts written in [python][1], DNA sequences were edited as follows: short sequence removal, primer pair removal and reversal to the correct orientation. Clean marker sequences were then clustered in operational taxonomic units (OTUs) and matched up against the [Genbank database][2]. All sequences and associated data were stored in a [biosql relational database][3], which was then queried to retrieve taxonomy assignments for each cluster. This is an illustration of the pipeline This is the link to the [project files](https://sourceforge.net/projects/appbiokth2011/files/) containing [data](https://sourceforge.net/projects/appbiokth2011/files/KTH_Project/Data/), [results](https://sourceforge.net/projects/appbiokth2011/files/KTH_Project/Results/), [Sarah's notebook](https://sourceforge.net/projects/appbiokth2011/files/KTH_Project/Sarahs%20notebook/), [Minttu's notebook](https://sourceforge.net/projects/appbiokth2011/files/KTH_Project/Minttus%20notebook/) and [paper](https://sourceforge.net/projects/appbiokth2011/files/KTH_Project/Paper/). </pre>MV2012Tue, 24 Jul 2012 14:11:10 -0000https://sourceforge.netbfdfd933687e8c5bd698b9b5b9fbfa0dc4a668behttps://sourceforge.net/p/appbiokth2011/wiki/Taxonomy%2520assignment/<pre>--- v29 +++ v30 @@ -1,4 +1,5 @@ -The aim of this project is to create an automated pipeline for the taxonomic assignment of DNA sequences from environmental samples. In this study, we focus on DNA markers amplified from benthic sediment samples. Using a series of customized scripts written in [python][1], DNA sequences were edited as follows: short sequence removal, primer pair removal and reversal to the correct orientation. Clean marker sequences were then clustered in operational taxonomic units (OTUs) and matched up against the [Genbank database][2]. All sequences and associated data were stored in a [biosql relational database][3], which was then queried to retrieve taxonomy assignments for each cluster. This is an illustration of the pipeline [https://sourceforge.net/p/appbiokth2011/wiki/Taxonomy%20assignment/#489f]. +The aim of this project is to create an automated pipeline for the taxonomic assignment of DNA sequences from environmental samples. In this study, we focus on DNA markers amplified from benthic sediment samples. Using a series of customized scripts written in [python][1], DNA sequences were edited as follows: short sequence removal, primer pair removal and reversal to the correct orientation. Clean marker sequences were then clustered in operational taxonomic units (OTUs) and matched up against the [Genbank database][2]. All sequences and associated data were stored in a [biosql relational database][3], which was then queried to retrieve taxonomy assignments for each cluster. This is an illustration of the pipeline ![PRoblem] (https://sourceforge.net/p/appbiokth2011/wiki/Taxonomy%20assignment/#489f) + This is the link to the [project files](https://sourceforge.net/projects/appbiokth2011/files/) containing [data](https://sourceforge.net/projects/appbiokth2011/files/KTH_Project/Data/), [results](https://sourceforge.net/projects/appbiokth2011/files/KTH_Project/Results/), [Sarah's notebook](https://sourceforge.net/projects/appbiokth2011/files/KTH_Project/Sarahs%20notebook/), [Minttu's notebook](https://sourceforge.net/projects/appbiokth2011/files/KTH_Project/Minttus%20notebook/) and [paper](https://sourceforge.net/projects/appbiokth2011/files/KTH_Project/Paper/). </pre>MV2012Tue, 24 Jul 2012 14:10:45 -0000https://sourceforge.net6650212e5e5232ca370f5cfa840b226083054eb8https://sourceforge.net/p/appbiokth2011/wiki/Taxonomy%2520assignment/<pre>--- v28 +++ v29 @@ -1,4 +1,4 @@ -The aim of this project is to create an automated pipeline for the taxonomic assignment of DNA sequences from environmental samples. In this study, we focus on DNA markers amplified from benthic sediment samples. Using a series of customized scripts written in [python][1], DNA sequences were edited as follows: short sequence removal, primer pair removal and reversal to the correct orientation. Clean marker sequences were then clustered in operational taxonomic units (OTUs) and matched up against the [Genbank database][2]. All sequences and associated data were stored in a [biosql relational database][3], which was then queried to retrieve taxonomy assignments for each cluster. This is an illustration of the pipeline [We need a link to the figure here]. +The aim of this project is to create an automated pipeline for the taxonomic assignment of DNA sequences from environmental samples. In this study, we focus on DNA markers amplified from benthic sediment samples. Using a series of customized scripts written in [python][1], DNA sequences were edited as follows: short sequence removal, primer pair removal and reversal to the correct orientation. Clean marker sequences were then clustered in operational taxonomic units (OTUs) and matched up against the [Genbank database][2]. All sequences and associated data were stored in a [biosql relational database][3], which was then queried to retrieve taxonomy assignments for each cluster. This is an illustration of the pipeline [https://sourceforge.net/p/appbiokth2011/wiki/Taxonomy%20assignment/#489f]. This is the link to the [project files](https://sourceforge.net/projects/appbiokth2011/files/) containing [data](https://sourceforge.net/projects/appbiokth2011/files/KTH_Project/Data/), [results](https://sourceforge.net/projects/appbiokth2011/files/KTH_Project/Results/), [Sarah's notebook](https://sourceforge.net/projects/appbiokth2011/files/KTH_Project/Sarahs%20notebook/), [Minttu's notebook](https://sourceforge.net/projects/appbiokth2011/files/KTH_Project/Minttus%20notebook/) and [paper](https://sourceforge.net/projects/appbiokth2011/files/KTH_Project/Paper/). </pre>MV2012Tue, 24 Jul 2012 14:09:31 -0000https://sourceforge.net85527bf9f09fa05c7e2167a159b8815661b04c64https://sourceforge.net/p/appbiokth2011/wiki/Taxonomy%2520assignment/<pre>--- v27 +++ v28 @@ -1,4 +1,4 @@ -The aim of this project is to create an automated pipeline for the taxonomic assignment of DNA sequences from environmental samples. In this study, we focus on DNA markers amplified from benthic sediment samples. Using a series of customized scripts written in [python][1], DNA sequences were edited as follows: short sequence removal, primer pair removal and reversal to the correct orientation. Clean marker sequences were then clustered in operational taxonomic units (OTUs) and matched up against the [Genbank database][2]. All sequences and associated data were stored in a [biosql relational database][3], which was then queried to retrieve taxonomy assignments for each cluster. This is an illustration of the pipeline [Virkki&Bourlat_Figure_1]. +The aim of this project is to create an automated pipeline for the taxonomic assignment of DNA sequences from environmental samples. In this study, we focus on DNA markers amplified from benthic sediment samples. Using a series of customized scripts written in [python][1], DNA sequences were edited as follows: short sequence removal, primer pair removal and reversal to the correct orientation. Clean marker sequences were then clustered in operational taxonomic units (OTUs) and matched up against the [Genbank database][2]. All sequences and associated data were stored in a [biosql relational database][3], which was then queried to retrieve taxonomy assignments for each cluster. This is an illustration of the pipeline [We need a link to the figure here]. This is the link to the [project files](https://sourceforge.net/projects/appbiokth2011/files/) containing [data](https://sourceforge.net/projects/appbiokth2011/files/KTH_Project/Data/), [results](https://sourceforge.net/projects/appbiokth2011/files/KTH_Project/Results/), [Sarah's notebook](https://sourceforge.net/projects/appbiokth2011/files/KTH_Project/Sarahs%20notebook/), [Minttu's notebook](https://sourceforge.net/projects/appbiokth2011/files/KTH_Project/Minttus%20notebook/) and [paper](https://sourceforge.net/projects/appbiokth2011/files/KTH_Project/Paper/). </pre>Sarah BourlatTue, 24 Jul 2012 06:39:15 -0000https://sourceforge.net6355fbb01a3ad6832a660a5249990f955ea8f564https://sourceforge.net/p/appbiokth2011/wiki/Taxonomy%2520assignment/<pre></pre>Sarah BourlatMon, 23 Jul 2012 17:19:37 -0000https://sourceforge.net34ff4767ddccece9f764ce402bd6739cba8b6918https://sourceforge.net/p/appbiokth2011/wiki/Taxonomy%2520assignment/<pre>--- v25 +++ v26 @@ -1,6 +1,6 @@ The aim of this project is to create an automated pipeline for the taxonomic assignment of DNA sequences from environmental samples. In this study, we focus on DNA markers amplified from benthic sediment samples. Using a series of customized scripts written in [python][1], DNA sequences were edited as follows: short sequence removal, primer pair removal and reversal to the correct orientation. Clean marker sequences were then clustered in operational taxonomic units (OTUs) and matched up against the [Genbank database][2]. All sequences and associated data were stored in a [biosql relational database][3], which was then queried to retrieve taxonomy assignments for each cluster. This is an illustration of the pipeline [Virkki&Bourlat_Figure_1]. -This is the link to the project files [kthproject](https://sourceforge.net/projects/appbiokth2011/files/) containing [data](https://sourceforge.net/projects/appbiokth2011/files/KTH_Project/Data/), [results](https://sourceforge.net/projects/appbiokth2011/files/KTH_Project/Results/), [Sarah's notebook](https://sourceforge.net/projects/appbiokth2011/files/KTH_Project/Sarahs%20notebook/), [Minttu's notebook](https://sourceforge.net/projects/appbiokth2011/files/KTH_Project/Minttus%20notebook/) and [paper](https://sourceforge.net/projects/appbiokth2011/files/KTH_Project/Paper/). +This is the link to the [project files](https://sourceforge.net/projects/appbiokth2011/files/) containing [data](https://sourceforge.net/projects/appbiokth2011/files/KTH_Project/Data/), [results](https://sourceforge.net/projects/appbiokth2011/files/KTH_Project/Results/), [Sarah's notebook](https://sourceforge.net/projects/appbiokth2011/files/KTH_Project/Sarahs%20notebook/), [Minttu's notebook](https://sourceforge.net/projects/appbiokth2011/files/KTH_Project/Minttus%20notebook/) and [paper](https://sourceforge.net/projects/appbiokth2011/files/KTH_Project/Paper/). This is the link to the [python code](https://sourceforge.net/p/appbiokth2011/code/ci/78249081e205a0142525f036bb9fcced0690eb6e/tree/) </pre>Sarah BourlatMon, 23 Jul 2012 17:11:18 -0000https://sourceforge.net91826490e79e137ab596235dc3d2b95f6238e79e