SEA-PHAGES | BLAST notes: PhagesDB or GenBank?

Link to this post \| posted 23 Feb, 2016 15:48
fbaliraine	Just to be sure: Does BLAST in the DNA Master description (BLAST: Matches Phage gp##, q#:s# Aligns with PhageName gp## q##:s##) strictly refer to BLASTp in NCBI/DNA Master or could it be also in PhageDb? The reason I am asking is because in some cases DNA Master may show a q1:s1 match for a phage but in some cases when I change the start position from the one originally called by Glimmer/GeneMark, I get a q1:s1 in PhagesDb but not in NCBI. For example for position in Gideon_draft 28917 bp start position (Original Glimmer call @bp 2872 gives a 100% match, q1:s1, E=0.0 with integrase (Y-int) of Phages Phreak, Gomashi, Frosty24, Cedasite, Avrafan, Annihilator, Hope, and Angel in phagesDb, but in NCBI, the top hit is Integrase of Mycobacterium abscessus q66:s2, E = 9e-120 over 61% of the protein.

Link to this post | posted 23 Feb, 2016 15:48

Just to be sure: Does BLAST in the DNA Master description (BLAST: Matches Phage gp##, q#:s#
Aligns with PhageName gp## q##:s##) strictly refer to BLASTp in NCBI/DNA Master or could it be also in PhageDb? The reason I am asking is because in some cases DNA Master may show a q1:s1 match for a phage but in some cases when I change the start position from the one originally called by Glimmer/GeneMark, I get a q1:s1 in PhagesDb but not in NCBI. For example for position in Gideon_draft 28917 bp start position (Original Glimmer call @bp 2872 smile

gives a 100% match, q1:s1, E=0.0 with integrase (Y-int) of Phages Phreak, Gomashi, Frosty24, Cedasite, Avrafan, Annihilator, Hope, and Angel in phagesDb, but in NCBI, the top hit is Integrase of Mycobacterium abscessus q66:s2, E = 9e-120 over 61% of the protein.

Link to this post \| posted 24 Feb, 2016 15:00
welkin	It does not strictly refer to NCBI. Frankly, I would prefer the phagesdb match over a random gene in GenBank that was likely deposited by auto-annotation software with no personal review. The matches retrieved by BLAST at NCBI are also sorted according to age; identical newer hits are listed first. The point of listing the BLAST data is to demonstrate that you are examining similar genes and looking to see which starts have been used previously. Using the top hit for your notes is a convenience rather than a requirement: GenBank used to only list our phages rather than tons of auto-annotated prophages, so it didn't really matter where you got the alignment from. Noting the alignment of your gene to similar phage gene makes much more sense to me!

Link to this post | posted 24 Feb, 2016 15:00

welkin

It does not strictly refer to NCBI. Frankly, I would prefer the phagesdb match over a random gene in GenBank that was likely deposited by auto-annotation software with no personal review.

The matches retrieved by BLAST at NCBI are also sorted according to age; identical newer hits are listed first. The point of listing the BLAST data is to demonstrate that you are examining similar genes and looking to see which starts have been used previously. Using the top hit for your notes is a convenience rather than a requirement: GenBank used to only list our phages rather than tons of auto-annotated prophages, so it didn't really matter where you got the alignment from. Noting the alignment of your gene to similar phage gene makes much more sense to me!

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BLAST notes: PhagesDB or GenBank?