I am intending to do a sequencing of a gene and to detect possible mutations in the coding region. I've seen many commercial software which are much more complex to use. What I need is a free, easy to use software to analyse the sample sequence with the reference from NCBI and to decide it's zygosity. The software should give a nice graphical representation of the mutation and the details of amino acid substitutions if any. Please note, that's all I need from that software and doesn't require any complex analysis.
I use Vector NTI for sequence comparisons.
For mutation detection you can use Alalmut software
Vector NTI works, but you may also try biology work bench (http://workbench.sdsc.edu/) . This is free software that is run by the San Diego Super Computer. It sounds like you may also benefit from using ClustalW (http://www.ebi.ac.uk/Tools/msa/clustalw2/) in combination with the ExPASy protein translation tool (http://web.expasy.org/translate/)
Thanks Zachary Tackett, That helps a lot. I have a very simple question for you. Since you've talked about the protein translation, what do you use to analyse the structure of a protein from a particular mRNA or to characterize the structural differences of the protein resultant from the TEST with the W/T or Ref protein? Thanks in advance
Sorry it took so long to get back to you Harindra. I had to be away from the computer for a few days, and when I got back to it it took me a while to find your message. The question also depends on the type of protein you are working with. It is very difficult to predict the structure of a protein based on the sequence. In fact my understanding is there is an annual contest each year to see which company can develop software that comes the closest. My next question is do you have x-ray crystallography data, or are you wanting to predict primarily secondary structure (which can more easily be predicted by computer algorithms).
I guess in order to answer your question more accurately I would need to know what type of protein you are working with. For instance a transmembrane protein is going to require a different approach from a metabolic enzyme.
Based on the generalities I've assumed from what I've read so far here are a few general ideas.
1. Try a motif search- motifs are patterns in a section protein's sequence that are characteristic of a proteins function or structure. For instance there are ATP binding motifs, transmembrane segment motifs, and many more. I usually don't have a favorite software for this, but Prosite has generally been pretty reliable in the past.
http://prosite.expasy.org
PRATT - allows to interactively generate conserved patterns from a series of unaligned proteins (also found on the above webpage).
2. You can try entering your sequences into biology workbench. This is a free bioinformatics program you can sign up for that uses the San Diego Super computer for alignment and motif search. It is pretty self explanatory and can be found at http://workbench.sdsc.edu.
Also biology workbench has a scan tool to look for secondary structure characteristics such as alpha helices, and beta pleated sheets.
Hope this helps,
Zach
Thanks Zachary for getting back to me and for your comprehensive answer. What I'm interested in is called TACI (http://www.ncbi.nlm.nih.gov/protein/BAE16555.1), which is encoded by 5 exons and has a trans-membrane region. I have no previous experiences with protein chemistry and hoping to carry out a fundamental study on mutations in TACI which is pretty common in CVID patients. Basically I want to compare the structural differences in mutated proteins with the ref. No I don't have any x ray crystallography details. At the end of the day I just want to show that possible mutations in trans-membrane or conserved regions may have been responsible for the impaired surface expression while mutations in other regions (ligand binding) has no any impact on the expression of the protein.
Please advice me accordingly
Harindra
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