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Guan_Practice with basic bioinformatics #1

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279f263
align sigma70.ref
xyguan15 Oct 9, 2022
5ec4095
Build a profile HMM for sigma70_align
xyguan15 Oct 9, 2022
02d0482
Search results for Roseobacter.fasta in sigma_Pro
xyguan15 Oct 9, 2022
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20 changes: 20 additions & 0 deletions Roseo_match
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Original file line number Diff line number Diff line change
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# --- full sequence ---- --- best 1 domain ---- --- domain number estimation ----
# target name accession query name accession E-value score bias E-value score bias exp reg clu ov env dom rep inc description of target
# ------------------- ---------- -------------------- ---------- --------- ------ ----- --------- ------ ----- --- --- --- --- --- --- --- --- ---------------------
tr|B7RH33|B7RH33_9RHOB - sigma70_align - 6.1e-24 81.5 0.4 1.4e-23 80.4 0.4 1.6 1 0 0 1 1 1 1 -
tr|B7RGX5|B7RGX5_9RHOB - sigma70_align - 3.5e-20 69.5 0.1 7e-20 68.5 0.1 1.6 1 0 0 1 1 1 1 -
tr|B7RH17|B7RH17_9RHOB - sigma70_align - 4.4e-19 66.0 0.2 1.1e-18 64.7 0.2 1.7 1 0 0 1 1 1 1 -
tr|B7RJL9|B7RJL9_9RHOB - sigma70_align - 9.2e-19 64.9 0.2 1.6e-18 64.1 0.2 1.4 1 0 0 1 1 1 1 -
tr|B7RI57|B7RI57_9RHOB - sigma70_align - 1.3e-18 64.4 0.5 6.7e-18 62.2 0.2 2.1 2 0 0 2 2 2 1 -
tr|B7RH51|B7RH51_9RHOB - sigma70_align - 2.5e-17 60.4 0.1 5e-17 59.4 0.1 1.5 1 0 0 1 1 1 1 -
tr|B7RSA6|B7RSA6_9RHOB - sigma70_align - 1.3e-14 51.6 0.4 2.5e-14 50.8 0.4 1.4 1 0 0 1 1 1 1 -
#
# Program: hmmsearch
# Version: 3.3.2 (Nov 2020)
# Pipeline mode: SEARCH
# Query file: sigma_Pro
# Target file: Roseobacter.fasta
# Option settings: /afs/crc.nd.edu/user/x/xguan4/Private/BioComputing2022/tools/hmmsearch --tblout Roseo_match sigma_Pro Roseobacter.fasta
# Current dir: /afs/crc.nd.edu/user/x/xguan4/Private/BioComputing2022/Exercise7/Bioinformatics_Walkthrough
# Date: Sun Oct 9 11:09:23 2022
# [ok]
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