@@ -14,6 +14,21 @@ The official EMBOSS suite comprises of over 150 programs that are available as c
Wageningen Bioinformatics Webportal, Netherlands offers [a graphical user interface to the EMBOSS suite](http://emboss.bioinformatics.nl/cgi-bin/emboss/), which we will use today for the hands-on session (more like demo!).
## Quick Demo on EMBOSS tools
...but before that, re-use/do the Clustal Omega analysis on your set of 10 P53 sequences. (or, go down this document to use my set of sequences ;) !)
- Swich to [Mview](http://www.ebi.ac.uk/Tools/msa/mview/) to visualize consensus
- Also check [alnviz](https://toolkit.tuebingen.mpg.de/alnviz), but don''t dive into it today. We will cover such visualizations tomorrow.
- Create consensus with [cons](http://emboss.bioinformatics.nl/cgi-bin/emboss/cons)
- Also check [consambig](http://emboss.bioinformatics.nl/cgi-bin/emboss/consambig): cons calculates a consensus sequence from a multiple sequence alignment. To obtain the consensus, the amino acid residue or nucleotide at each position is compared to the possible ambiguity codes using consambig. The consensus sequence uses the minimum ambiguity code match. The ambiguity characters were designed to encode positional variations found among families of related genes. Useful for DNA sequences.
- use [Merger](Merge two overlapping sequences) to merge two overlapping sequences. It uses a global alignment algorithm (Needleman & Wunsch) to optimally align the sequences. A merged sequence is generated from the alignment and writen to the output file. Also useful in case of DNA.
-[Dotmatcher](http://emboss.bioinformatics.nl/cgi-bin/emboss/dotmatcher) generates a dotplot from two input sequences. The dotplot is an intuitive graphical representation of the regions of similarity between two sequences. All positions from the first input sequence are compared with all positions from the second input sequence using a specified substitution matrix.
- Swich to [Mview](http://www.ebi.ac.uk/Tools/msa/mview/) to visualize consensus
- Create consensus with [cons](http://emboss.bioinformatics.nl/cgi-bin/emboss/cons)
- Also check [consambig](http://emboss.bioinformatics.nl/cgi-bin/emboss/consambig): cons calculates a consensus sequence from a multiple sequence alignment. To obtain the consensus, the amino acid residue or nucleotide at each position is compared to the possible ambiguity codes using consambig. The consensus sequence uses the minimum ambiguity code match. The ambiguity characters were designed to encode positional variations found among families of related genes. Useful for DNA sequences.
- use [Merger](Merge two overlapping sequences) to merge two overlapping sequences. It uses a global alignment algorithm (Needleman & Wunsch) to optimally align the sequences. A merged sequence is generated from the alignment and writen to the output file. Also useful in case of DNA.
-[Dotmatcher](http://emboss.bioinformatics.nl/cgi-bin/emboss/dotmatcher) generates a dotplot from two input sequences. The dotplot is an intuitive graphical representation of the regions of similarity between two sequences. All positions from the first input sequence are compared with all positions from the second input sequence using a specified substitution matrix.
