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linnabrown / run_dbcan

Run_dbcan V4, using genomes/metagenomes/proteomes of any assembled organisms (prokaryotes, fungi, plants, animals, viruses) to search for CAZymes.
http://bcb.unl.edu/dbCAN2
GNU General Public License v3.0
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output explanations #148

Open CamiAgustini opened 8 months ago

CamiAgustini commented 8 months ago

Hi @linnabrown , @yinlabniu , @AaronAOliver

Thank you for this great resource! I am looking through the output of run_dbcan script and was wondering if you could guide me in the right direction.

Can you explain me the meaning of: -Diamond: CE8+PL1+4.2.2. (is is that both are probably?) -e-CAMI: GH120+GH51+CBM6 -HMMER: CE20(113363)+GH43_16(502812)+CBM6(837952) (what are the numers in brakets?)

yinlabniu commented 8 months ago

Can you let us know which output file you are referring to? A screenshot would be the best.

Yanbin

From: CamiAgustini @.> Sent: Monday, January 8, 2024 1:06 PM To: linnabrown/run_dbcan @.> Cc: Yanbin Yin @.>; Mention @.> Subject: [linnabrown/run_dbcan] output explanations (Issue #148)

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Hi @linnabrownhttps://urldefense.com/v3/__https://github.com/linnabrown__;!!PvXuogZ4sRB2p-tU!GBpPqSK9W5wIEczdCzNknjyosGkQLi-Q__rgZyCr8Ha2bfNp-u-QtZhcjiPUEey7BZ6E-h-JZ3jfNv31XuUGjQ$ , @yinlabniuhttps://urldefense.com/v3/__https://github.com/yinlabniu__;!!PvXuogZ4sRB2p-tU!GBpPqSK9W5wIEczdCzNknjyosGkQLi-Q__rgZyCr8Ha2bfNp-u-QtZhcjiPUEey7BZ6E-h-JZ3jfNv2yGYbALg$ , @AaronAOliverhttps://urldefense.com/v3/__https://github.com/AaronAOliver__;!!PvXuogZ4sRB2p-tU!GBpPqSK9W5wIEczdCzNknjyosGkQLi-Q__rgZyCr8Ha2bfNp-u-QtZhcjiPUEey7BZ6E-h-JZ3jfNv1bSFc4ag$

Thank you for this great resource! I am looking through the output of run_dbcan script and was wondering if you could guide me in the right direction.

Can you explain me the meaning of: -Diamond: CE8+PL1+4.2.2. (is is that both are probably?) -e-CAMI: GH120+GH51+CBM6 -HMMER: CE20(113363)+GH43_16(502812)+CBM6(837952) (what are the numers in brakets?)

— Reply to this email directly, view it on GitHubhttps://urldefense.com/v3/__https://github.com/linnabrown/run_dbcan/issues/148__;!!PvXuogZ4sRB2p-tU!GBpPqSK9W5wIEczdCzNknjyosGkQLi-Q__rgZyCr8Ha2bfNp-u-QtZhcjiPUEey7BZ6E-h-JZ3jfNv0G9dpiHg$, or unsubscribehttps://urldefense.com/v3/__https://github.com/notifications/unsubscribe-auth/AEXNKZRTZS5SOXSV4HKPCKLYNQ7TVAVCNFSM6AAAAABBR5ZIX2VHI2DSMVQWIX3LMV43ASLTON2WKOZSGA3TCMBVGU4TANQ__;!!PvXuogZ4sRB2p-tU!GBpPqSK9W5wIEczdCzNknjyosGkQLi-Q__rgZyCr8Ha2bfNp-u-QtZhcjiPUEey7BZ6E-h-JZ3jfNv1lPl2OHQ$. You are receiving this because you were mentioned.Message ID: @.***>

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CamiAgustini commented 8 months ago

Hi Yanbin,

Thank you for your message. Apologies for any confusion. I am referring to the output file generated during the data analysis process. Attached is a screenshot for clarity. [image: dbCAN2.png] [image: dbCAN.png] Feel free to reach out if you have further questions or need more information.

El lun, 8 ene 2024 a la(s) 4:10 p.m., Yanbin Yin @.***) escribió:

Can you let us know which output file you are referring to? A screenshot would be the best.

Yanbin

From: CamiAgustini @.> Sent: Monday, January 8, 2024 1:06 PM To: linnabrown/run_dbcan @.> Cc: Yanbin Yin @.>; Mention @.> Subject: [linnabrown/run_dbcan] output explanations (Issue #148)

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Hi @linnabrown< https://urldefense.com/v3/__https://github.com/linnabrown__;!!PvXuogZ4sRB2p-tU!GBpPqSK9W5wIEczdCzNknjyosGkQLi-Q__rgZyCr8Ha2bfNp-u-QtZhcjiPUEey7BZ6E-h-JZ3jfNv31XuUGjQ$> , @yinlabniu< https://urldefense.com/v3/__https://github.com/yinlabniu__;!!PvXuogZ4sRB2p-tU!GBpPqSK9W5wIEczdCzNknjyosGkQLi-Q__rgZyCr8Ha2bfNp-u-QtZhcjiPUEey7BZ6E-h-JZ3jfNv2yGYbALg$> , @AaronAOliver< https://urldefense.com/v3/__https://github.com/AaronAOliver__;!!PvXuogZ4sRB2p-tU!GBpPqSK9W5wIEczdCzNknjyosGkQLi-Q__rgZyCr8Ha2bfNp-u-QtZhcjiPUEey7BZ6E-h-JZ3jfNv1bSFc4ag$>

Thank you for this great resource! I am looking through the output of run_dbcan script and was wondering if you could guide me in the right direction.

Can you explain me the meaning of: -Diamond: CE8+PL1+4.2.2. (is is that both are probably?) -e-CAMI: GH120+GH51+CBM6 -HMMER: CE20(113363)+GH43_16(502812)+CBM6(837952) (what are the numers in brakets?)

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linnabrown commented 8 months ago

We already replaced the eCAMI with dbcan_sub for one year. Please update the new version for our dbcan tool. Thank you very much!