SEA-PHAGES | ORFs with BLAST match but without coding potential

Link to this post \| posted 12 Feb, 2018 19:27
ptsourkas	We have found 4 ORFs located in coding gaps that have significant BLAST matches (<E-10) to other Mycobacterium smegmatis phage genes, but without any coding potential. To call or not to call? The BLAST matches are as follows: ORF 1: gp57 in Mycobcterium phage Send513 with E-value = E-38 gp57 in Mycobcterium phage Papyrus with E-value = E-38 ORF 2: Many matches to HNH endonucleases in many Mycobacterium phages, all with E-value 0 ORF 3: gp90 in Mycobacterium phage Send 513 with E-value = E-13 ORF 4: gp72 in Mycobacterium phage Squirty with E-value = E-27 gp49 in Mycobacterium phage Shuna with E-value = E-21 Thanks for any insight.

Link to this post | posted 12 Feb, 2018 19:27

We have found 4 ORFs located in coding gaps that have significant BLAST matches (<E-10) to other Mycobacterium smegmatis phage genes, but without any coding potential. To call or not to call?
The BLAST matches are as follows:

ORF 1:
gp57 in Mycobcterium phage Send513 with E-value = E-38
gp57 in Mycobcterium phage Papyrus with E-value = E-38

ORF 2:
Many matches to HNH endonucleases in many Mycobacterium phages, all with E-value 0

ORF 3:
gp90 in Mycobacterium phage Send 513 with E-value = E-13

ORF 4:
gp72 in Mycobacterium phage Squirty with E-value = E-27
gp49 in Mycobacterium phage Shuna with E-value = E-21

Thanks for any insight.

Link to this post \| posted 12 Feb, 2018 22:25
grosasacosta	I am having issues with Starterator. I've been trying to run it for Hegedechwinu but it keeps crashing when it reaches Pham 92 (near the end of the analysis). Any suggestion on how to solve this issue? It is related to that specific Pham. From what I saw in other similar posts, the solution may not be simple at all. Please let me know if you have any suggestions on how to solve this issue, I will be waiting.

Link to this post | posted 12 Feb, 2018 22:25

grosasacosta

I am having issues with Starterator. I've been trying to run it for Hegedechwinu but it keeps crashing when it reaches Pham 92 (near the end of the analysis). Any suggestion on how to solve this issue? It is related to that specific Pham. From what I saw in other similar posts, the solution may not be simple at all. Please let me know if you have any suggestions on how to solve this issue, I will be waiting.

Link to this post \| posted 13 Feb, 2018 18:00
cdshaffer	Not every gene that codes for a protein will show strong GeneMarkS potential. For a discussion of this see the forum page on Typical vs atypical GeneMarkS coding potential: https://seaphages.org/forums/topic/75/ But the bottom line is that Coding potential is based on looking at very long orfs in the genome itself to determine the sequence characteristics of a "typical" gene, it then uses that definition to score every region of the genome to indicate how closely it matches the "typical" result. Not all genes are expected to be "typical" so lack of coding potential is not good evidence for lack of a gene. See the discussion posted above for more details. As for Starterator, I have reposted your question to the Starterator section of the forum: https://seaphages.org/forums/topic/4500/ Edited 13 Feb, 2018 18:16

Link to this post | posted 13 Feb, 2018 18:00

cdshaffer

Not every gene that codes for a protein will show strong GeneMarkS potential. For a discussion of this see the forum page on Typical vs atypical GeneMarkS coding potential:

https://seaphages.org/forums/topic/75/

But the bottom line is that Coding potential is based on looking at very long orfs in the genome itself to determine the sequence characteristics of a "typical" gene, it then uses that definition to score every region of the genome to indicate how closely it matches the "typical" result. Not all genes are expected to be "typical" so lack of coding potential is not good evidence for lack of a gene. See the discussion posted above for more details.

As for Starterator, I have reposted your question to the Starterator section of the forum:

https://seaphages.org/forums/topic/4500/

Edited 13 Feb, 2018 18:16

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ORFs with BLAST match but without coding potential