Please help me in prediction of new protein sequences I am a student of BS bioinformatic and this is my final project to predict novel protein seq and make an entry in any database I am totally confused what can one do I don't know the specific procedure and tools name. Please help me to perform the above task your suggestion will be very precious for me.
i am working on rice genome so please tell me the tools names that will predict the genes for rice
you have know your start and stop codons- on the DNA sequence to look for genes . and once you have the genes - you copy paste in PDB to translate into proteins.
so you will have the protein- and for identifying genes from proteins you need to know the name of the protein and search databases for its gene.
If you have the amino acid sequence of the protein, you can refer to databases to find the mRNA sequence or use the genetic code to work it out. Once you have the mRNA sequence, you can work out the gene's polynuceotide sequence by by reverse transcription. You can refer to existing databases to confirm the identity of the gene, especially if it is already known.
You may check these links for ideas. Tools names and ideas are provided in these links:
http://rice.plantbiology.msu.edu/auto_annot_pipeline.shtml
http://ricegaas.dna.affrc.go.jp/
Use these the mentioned tools to predict the genes from the sequence. Once you have the genes ,compare these genes with already established genes of rice genome
(download from sites . sample links : ftp://ftp.ensemblgenomes.org/pub/plants/release-27/fasta/oryza_sativa/cds/ and
http://rice.plantbiology.msu.edu/cgi-bin/gbrowse/rice/).
If no match is found, it may be possible to get a new novel gene.
Alternately, you may translate all the genes into corresponding proteins and compare them with the existing proteins of rice genome.
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