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7.3 years ago
poojaharshan133
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0
I am doing my masters in biotechnology in Kerala, India. I would like to get a flow chart on how to approach in completing my project. please do help me. I am looking into the papers like reconstruction protocol of Rongsirikul and also Starch biosynthesis pathways a comparative genomics approach by Saithong. Can you please help me.
This is not really a specific question, you'll get better help if you'll have a specific question. I'll suggest to start by making a list of the available and relevant databases - which genomes/transcriptomes are available, genes in this pathways in model organisms etc.
actually i ll put a brief of my reference work over here. Starch biosynthesis genes were collected from 5 template plants viz Arabidopsis, rice, maize, castor bean and potato. cassava genome was collected from phytozome database. using sequence similarity technique, blast template preparation was carried out. Reciprocal BLASTp was done then. then Function assignment was carried out. this is the first draft of starch biosynthesis pathway in cassava. Thenthe next step was defining the confidence of the pathway and calculating the confidence score.the reconstructed pathway was validated using the experimentally identified sequences. protein motif analysis was carried out.A final starch metabolic pathway was createdfollowed by pathway visualization. a descriptive map was prepared in SMART DRAW tool.at last the transcriptome data was integrated into the pathway to create an interactive map (VANTED). Fianlly an integrative map was made which is the output.
My queries are : 1) How to identify new genes insilico? 2) How to do reciprocal BLASTp? 3) How to identify orthologs in different species? 4) Apart from genes, which are the other components that could be incorporated into the reference pathway to reconstruct the pathway? 5) Which are the softwares used for reconstruction and mapping? 6) How to assign function to the genes? 7) Is BLAST2go is a good tool to perform my entire work?
To answer your questions should take an entire semester, or the new biostars e-book :)
how to get the new biostars ebook? Can you send me the link to download it please?
See this post The Biostar Handbook. A bioinformatics e-book for beginners.