Gene Number Comparison

Creating of a gene number cross reference between versions is complicated any or all of the following reasons:

1. Two genes become one - As contigs assemble, a partial gene at the end of one contig can assemble with a partial gene at the end of a different contig.
2. Two genes become one - As the sequence is polished, changes to a stop, insertions, and deletions can cause two genes to be in frame and now form one gene.
3. One gene becomes two - As the sequence is polished, insertions, deletions, and new stops can cause a gene to be split between two frames and now be two gene calls.
4. A gene disappears - As the sequence is polished, a frame change or stop occurs so close to the start of a gene that it doesn't get predicted in the new assembly.
5. A gene gets added - A new sequence may have new opportunities for genes which were not present in the previous build.

The columns are:

1. Gene from the new assembly
2. Length of gene from new assembly
3. Gene from the old assembly
4. Length of gene from old assembly
5. Type of hit -
   • When a gene from the old assembly and a gene from the new assembly list each other as their top hit, they are listed as "Two-way best hit".
   • If the best hit appears to be one way, it will show the best hit in that one direction. For example the Draft may have a best blast hit in the Finished but not the other way around. Often this occurs when there are two or more similar genes. For example:

     Finished Gene	Length	Draft Gene	Length	Type Hit	Length Comparison	Percent Identity
     Asuc1441	356	Draft0910	334	Finished hit Draft	longer	38
     Asuc1586	334	Draft0910	334	Two-way best hit	Same	100

     In this case gene Asuc1441 has a best Blast hit in the draft of Draft0910 which isn't reciprocated. This is because Draft0910 was a much better match to Asuc1586. The two finished genes Asuc1441 and Asuc1586 are probably similar but only one of them was represented in the draft version.
   • If there was no blast hit above the cutoff, it will say "no hit"
6. Comparison of the two gene lengths (e.g., may be different)
7. Percent Identity over the length of the alignment