How to do annotation after gene prediction?

garethboy

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#1

How to do annotation after gene prediction?

02-04-2014, 12:50 AM

Dear all,

I am pretty new in bioinformatics. I want to ask, after I perform gene prediction using PRODIGAL, I got the following:

PHP Code:

>final_001_R1_00001 # 2 # 898 # 1 # ID=1_1;partial=10;start_type=Edge;rbs_motif=None;rbs_spacer=None;gc_cont=0.644 ATGCCAGCAGGTCGATTGGCCAAGCCACTGGAGGCAATCGCGGGCCCGCTGCGGCGGTCA TCGCCGGAGTCCGTTGACCGGATGCTCATCGGCTTGTGCGCGGTCATCTGGTTGGCGTTC GTCGGGATGCTGGTCGGTGCCATCGTGGTGATCGCCGGAATGGGGGAGGACTCGGGTTCG TCGGGGTCTTCGTGGGGCATCTACATCGTCATCGGGGTATCGCTGGCCGTCATCGTCGGT GCCGTGCCGCTGTTGCTACGTGCCCGCAACACCGCTGCCCAGCGCACCTCGAAAACGGCC CCTAAAACCAAGGGCGCCAATTCCTCCGGTGGGGCCACTGCGCCGTCTGGACCGCCTCCC GCGGAGGCGTCGACCGAGAAGCTCAAGACCTTCGGTGGTCTCGCCGATCACGTGAGCCAT GTTCCCAAGGACTACAACGGTCCTGGGTCACCCGCGTACCGGGCAGCCACCGAGGCGGCC GCGAAGAGGGCGGTGGTCAACCGGCTGTGGTTGCGGGCCACGGTGGGGATCGCCGGCGCG ATCGGCCTGGCACTGCTGGCGGTGGTGACCGGTACCTATCTGCTGGCAGTGGAAAGCGAC ACCGCCGCCATCGTCGCGTTCGTCTTCGCCGGGGTGATCACCTGCGCGATGGGGGCCATT CCATGGGTGACGCTCAAGAAGCTGCGCGAGCTCGGCTCGTCGGGGTCTTAG

After I perform a local BLAST, how can I get something like the following?

PHP Code:

>final_001_R1_00001 hypothetical protein ATGCCAGCAGGTCGATTGGCCAAGCCACTGGAGGCAATCGCGGGCCCGCTGCGGCGGTCA TCGCCGGAGTCCGTTGACCGGATGCTCATCGGCTTGTGCGCGGTCATCTGGTTGGCGTTC GTCGGGATGCTGGTCGGTGCCATCGTGGTGATCGCCGGAATGGGGGAGGACTCGGGTTCG TCGGGGTCTTCGTGGGGCATCTACATCGTCATCGGGGTATCGCTGGCCGTCATCGTCGGT GCCGTGCCGCTGTTGCTACGTGCCCGCAACACCGCTGCCCAGCGCACCTCGAAAACGGCC CCTAAAACCAAGGGCGCCAATTCCTCCGGTGGGGCCACTGCGCCGTCTGGACCGCCTCCC GCGGAGGCGTCGACCGAGAAGCTCAAGACCTTCGGTGGTCTCGCCGATCACGTGAGCCAT GTTCCCAAGGACTACAACGGTCCTGGGTCACCCGCGTACCGGGCAGCCACCGAGGCGGCC GCGAAGAGGGCGGTGGTCAACCGGCTGTGGTTGCGGGCCACGGTGGGGATCGCCGGCGCG ATCGGCCTGGCACTGCTGGCGGTGGTGACCGGTACCTATCTGCTGGCAGTGGAAAGCGAC ACCGCCGCCATCGTCGCGTTCGTCTTCGCCGGGGTGATCACCTGCGCGATGGGGGCCATT CCATGGGTGACGCTCAAGAAGCTGCGCGAGCTCGGCTCGTCGGGGTCTTAG

In other words, after performing gene prediction, how to get a file which project the sequences as following?

PHP Code:

>gene_0001 GENE_NAME_A SEQUENCE... >gene_0002 GENE_NAME_B SEQUENCE... >gene_0003 GENE_NAME_C SEQUENCE... >gene_0004 GENE_NAME_D SEQUENCE... >gene_0005 GENE_NAME_E SEQUENCE... >gene_0006 GENE_NAME_F SEQUENCE...
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Desai

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Join Date: Dec 2013

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#2

02-04-2014, 03:26 AM

Dear garethboy

I dont't know how to get sequence like that but yes u can use BLAST2GO tool for mapping and annotation. could I know what is your conclusion?
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boetsie

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02-04-2014, 02:45 PM

Use a tool like Prokka (http://www.vicbioinformatics.com/software.prokka.shtml) to predict and annotate your sequences. After the genbank or other files are generated, write a script to add the annotation to your fastA file.

Boetsie
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