Example data for this tutorial............................................................................................................................................34
Interface choices..................................................................................................................................................................35
General points about working with bioinformatics programs.......................................................................................36
Sequence formats.............................................................................................................................................................36
File naming conventions in bioinformatics......................................................................................................................37
Naming files and the danger of over-writing previous results.........................................................................................39
A common problem: what is a text file and what is not...................................................................................................39
GZipped files in bioinformatics.......................................................................................................................................40
EXAMPLES OF RUNNING BIOINFORMATICS PROGRAMS ON BIO-LINUX..................41
Analysing sequences with QIIME.....................................................................................................................................41
Preparation.......................................................................................................................................................................42
Assign Samples to Multiplex Reads................................................................................................................................42
Processing sequences into OTUs.....................................................................................................................................43
Data to information..........................................................................................................................................................44
Heatmap......................................................................................................................................................................45
Taxonomy Summary Charts........................................................................................................................................45
Diversity...........................................................................................................................................................................45
Alpha...........................................................................................................................................................................45
Beta..............................................................................................................................................................................45
Inter-Sample Distance.................................................................................................................................................46
Jackknifing & UPGMA...............................................................................................................................................46
Analysing sequences with MOTHUR................................................................................................................................47
Preparation.......................................................................................................................................................................47
Assign Samples to Multiplex Reads and Quality Filtering..............................................................................................48
Generating Alignment & Distance Matrix.......................................................................................................................48
Classify Sequences...........................................................................................................................................................49
Renaming Files.................................................................................................................................................................49
Clustering Sequences.......................................................................................................................................................49
Generating OTU Table and Normalisation......................................................................................................................49
Classifying OTU..............................................................................................................................................................50
Converting the shared file to BIOM-format.....................................................................................................................50
Data to information..........................................................................................................................................................50
Heatmap......................................................................................................................................................................50
Venn Diagram..............................................................................................................................................................50
Finding and running useful scripts...................................................................................................................................51
Aligning sequences using MUSCLE..................................................................................................................................51
BLAST.................................................................................................................................................................................53
A few examples of ways to run BLAST, on Bio-Linux or otherwise.........................................................................53
What this course covers...............................................................................................................................................53
Why use BLAST on the command line?.....................................................................................................................53
General considerations for database searching...........................................................................................................54
A very, very brief introduction to BLAST+................................................................................................................54
How a BLAST database looks on the file system.......................................................................................................55
A simple blastp search.................................................................................................................................................55
Formatting BLAST output..........................................................................................................................................56
Handling multiple sequences......................................................................................................................................57
BLAST searching using fasta files containing more than one sequence................................................................57
Processing multiple files using a foreach loop..................................................................................................................57
Working with lots of BLAST results...........................................................................................................................61
EMBOSS Programs............................................................................................................................................................62
Ways to run EMBOSS programs:...............................................................................................................................62
A comparison of the Jemboss and command line interfaces for EMBOSS programs...........................................63
Working with EMBOSS programs..............................................................................................................................63
Using the EMBOSS command line.............................................................................................................................65
A very basic sequence assembly.........................................................................................................................................69
Quality Checking.........................................................................................................................................................69
Split Barcodes.............................................................................................................................................................69
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