How can we correlate the result of Blast N or Blast X or P with a novel gene. Are black lines in the Blast result significant to tell about novelty. What other in silico methods can one exploit for finding a novel gene.
Found the co-relation between the blast N and a novel gene product. The black lines in the result bar depict the novelty of the gene when we search against the Genomic Database and also the EST database. No significant similarity found as a blast hit also makes the gene count for novelty. As per the experience I would recommend to change the threshold values and window size length to recheck if still there is no existing gene within the GSS and EST database. Also make use of the exclude organism option as your experimental set-up.
To authenticate our validation for a novel hit, it's always recommended to do all 6 reading frame protein searches using Blast P or X.
Any further queries or comments are always welcomed. Please feel free to write.