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All posts created by Wabush
| Link to this post | posted 12 Mar, 2025 15:36 | |
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There are 4 phage genes in Pham 107875 (Note: the Pham# may change by the time this is read) which may have been incorrectly added - but I am not sure about this. They are: 1) CapnMurica_51, 2) Gordon_51, 3) MiniBagel_53, and 4) Teacup_54. Regardless, the genes downstream of the above genes were deleted and should be added. Reasons for Deleting the Above Genes: ————————————- 1) GeneMarkS and GeneMark files for each of the above genes shows no coding potential - or very minimal coding potential. (see attached image MiniBagel_gp53) 2) The above annotated genes overlap a gene that was deleted. The Reasons for keeping the Deleted Downstream Gene: —————————————————- 1) The deleted gene was identified by GeneMark and Glimmer, had high coding potential, had good RBS values (see attached image Minibagel_DeletedGene), and were in a Pham with 53 other genes (see the pham for Acai_gp53 I believe the annotator may have looked at the GeneMark file instead of the GeneMarkS file when making the decision as the GeneMark file is misleading and shows no coding potential. For example: ———— the deleted MiniBagel gene from 37872-38024 has high GeneMarkS coding potential, is supported by Glimmer and GeneMark, has good RBS values: spacer 10, z-score 2.436, and final score -3.814, and is in a Pham with 53 other phage genes. In addition, by keeping this gene the following gene will have a -4 gap. |
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118KbPosted in: Cluster AU Annotation Tips → Called Gene not a Gene
| Link to this post | posted 11 Mar, 2025 15:12 | |
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Thanks x 10^31 ! |
| Link to this post | posted 11 Mar, 2025 14:01 | |
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Hi Dan, Is the phage sequencing information you mentioned in your post still the same for phages sequenced in Jan 2025? Thanks, Kieran |
| Link to this post | posted 25 Mar, 2021 21:18 | |
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Hi Chris, Thank-you so much for the explanation. It was very nice of you to write such a nice detailed response. Very helpful indeed. Much appreciated! Kieran |
Posted in: Functional Annotation → Phage gene annotation has matching phage genes have 4 different proteins - which one is a match?
| Link to this post | posted 06 Mar, 2021 02:01 | |
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Wabush |
in PECAAN and I would like some guidance as to which protein function I should assign to the gene.Posted in: Functional Annotation → Phage gene annotation has matching phage genes have 4 different proteins - which one is a match?
| Link to this post | posted 06 Mar, 2021 02:01 | |
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I am annotating the phage Crewmate (gene 2 in PECAAN and I would like some guidance as to which protein function I should assign to the gene.- The NCBI BlastP of the gene returns several matching phages and their proteins. - (See the attached image for details) The first 9 phages returned have high coverage (99.28%-100%), high alignment (>96%), low e-values (0), and high identity (>90%). (see the attached image for details)but they have annotated 4 different proteins and I am unsure which one is a good reference for the Crewmate gene 28? The proteins assigned to the 9 phages are: - Cas4 family exonuclease (4 of 9 phages called this) - Exonuclease (3 of 9 phages called this) - RepA-like helicase (1 of 9 phages called this) - Hypothetical protein (1 of 9 phages called this) Thank-you kindly for reading and for any help offered, Kieran References: A. Attached to this post is a screen shot of NCBI Blastp in PECAAN B. Protein Sequence: MTTPKVSTIKRGGARFYVDPDDGKIKVPGVTSIIGMLPKEFLRYWAAKEVAQTAVDSLPTVLQMILNDQSDAAVDFLKKSPDRNTRKAADTGTAAHDLFERMAKGETVGRVHPDLEPFVRHFDEFLTVAKPEYHFLEETVWSDKHAYAGSFDAYATIGGERLWLDNKTTRSGIHEEVGIQLAAYRFADSIIRADGGRVPMPTADGGAVLHVRPEGWKLVPVRCDEELFEVFLHLREVFKYEKEIKSTIVGREVFSGPAEDAPTGPKRRTPRARKAAE |
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