I'm looking for a good software (free and/or commercial) to analyse my sample sequences with a refseq and see if there are any mutations, or the translated protein is affected. The software should be easy to use (good UI since I'm not a hardcore bioinformatic person) and should offer crucial information hassle free (SNP or mutation in standard annotation, Protein annotation). A sophisticated software which does similar to variobox. Thanks
http://bioinformatics.ua.pt/software/variobox/
Dear Harindra
Please read the article entitled "Mutation Surveyor Software for DNA Sequence Analysis" that shows step by step guide of how to use this program named Mutation Surveyor.
Best Regards
Dear Harindra
If you wish to learn more about different methods of detecting a mutation then here is a very good book entitled "PCR Mutation Detection Protocols" which enlists all different types of methods whether old or latest used by scientist for mutation detection.
I hope and wish that you will like this book.
Best Regards
Dear Afzal,
Thanks for your posts and documents. Will you also be able to suggest me a free easy to use mutation analyser as well?
Dear Harindra,
You can use Mutation taster, Polyphen2 and SIFT whic are free and reliable tools.
good luck
Dear Dr Arul,
Thanks for your suggestion. What I need is something similar to VarioBox where we can analyse our sequence against a refseq. It will also annotate the mutation accordingly and also indicate the affected protein.
If you already have the mutation file (VCF), you can use programme Afzal suggested. You can also try out KGGSeq (http://statgenpro.psychiatry.hku.hk/limx/kggseq/) which tried to combine those score to perform a prediction. It will also give information on domain and protein function etc.
However, if you haven't get the VCF file, you might want to use the Galaxy (http://galaxyproject.org/) to help you to perform the upstream analysis.
If you are interested and are willing to learn how to perform the whole analysis on Linux system, then you can have a look at GATK (http://www.broadinstitute.org/gatk/). They have a very good documentation and tutorial on http://www.broadinstitute.org/gatk/guide/best-practices
Disclaimer: KGGSeq is developed by the RAP in my lab
Dear Shing,
Really appreciate your suggestion. I'm a newbie for bioinformatics and still trying to figure out things about performing few analysis with those tools.
What I simply need is a free, easy to use, reliable software which can automatically detect mutations against a reference sequence. VarioBox is pretty good, but it can only analyse one sequence at a time.
What do you think?
Thanks
I have never used VarioBox before so I cannot comment on its performance. However, if you really want free programmes in bioinformatics, usually they will come in command line interface and rarely will they have GUI. It will be a good idea for you to try out some simple software and get a hang of how to work on them. GATK is good in a way that they have all the required command posted online. If you really don't want to go into the trouble with linux, I guess you can always use GALAXY. But it will always be a good idea to try and use the command line interface as you will soon find out that majority of the tools that are free, works on the command line interface.
We generally use a software called Alamut. It can also provide information about the SNP and mutations. You can get the details of SNP with reference number with one click. It is very reliable and easy to use in my field of research
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