[Inparanoid] Missing specific genes from InParanoid results
Justin Elser
elserj at science.oregonstate.edu
Tue Oct 14 23:57:15 CEST 2014
I am running InParanoid 3.0 (although I also tested under 4.1 to see if
it fixed my problem) and have the following issue. I am running
Arabidopsis thaliana vs Oryza sativa sp. japonica and mostly getting
results as I would expect. However, a few genes end up not getting
placed in a cluster at all, even though it looks like the blast results
show pretty good matches.
I have placed grepped blast results for AT5G49190 at the end of this
message. If I am understanding the scoring correctly, this gene shows a
high similarity score with AT4G02280 and OS03T0340500-01, which is what
I expect from an independent analysis using Compara (74% match).
However, when the script to place the genes in clusters is ran,
AT5G49190 does not show up in any cluster at all. There is a cluster
that does contain AT4G02280 and OS03T0340500-01. I'm hoping you guys can
help me figure out what is causing this.
Also, I thought I tried to subscribe to the mailing list last week, but
haven't seen anything back yet. If someone could check on this and let
me know if I missed something in my attempt, that would be great.
Let me know if you need any more information or things I can do to
diagnose this.
Thanks in advance,
justin
[elserj at waterman ]$ cat
Arabidopsis_thaliana_phytozome_mart_9_9_13.fa-Arabidopsis_thaliana_phytozome_mart_9_9_13.fa
| grep AT5G49190
AT5G37180.1 AT5G49190.1 894.0 836 807 788 791
788 791 q:14-801 h:15-805
AT4G10120.2 AT5G49190.1 166.4 1050 807 494 485
494 485 q:197-690 h:278-762
AT1G78800.1 AT5G49190.1 60.8 403 807 177 188
177 188 q:213-389 h:573-760
AT4G10120.1 AT5G49190.1 166.4 1050 807 494 485
494 485 q:197-690 h:278-762
AT4G02280.1 AT5G49190.1 1293.5 809 807 802 802
802 802 q:8-809 h:5-806
AT5G20830.2 AT5G49190.1 1139.8 808 807 799 802
799 802 q:10-808 h:5-806
AT1G73370.1 AT5G49190.1 932.2 942 807 803 802
803 802 q:11-813 h:5-806
AT5G49190.1 AT5G49190.1 1676.8 807 807 807 807
807 807 q:1-807 h:1-807
AT5G49190.1 AT4G02280.1 1293.5 807 809 802 802
802 802 q:5-806 h:8-809
AT5G49190.1 AT3G43190.1 1152.1 807 808 802 799
802 799 q:5-806 h:10-808
AT5G49190.1 AT5G20830.1 1124.4 807 808 802 799
802 799 q:5-806 h:10-808
AT5G49190.1 AT5G20830.2 1124.4 807 808 802 799
802 799 q:5-806 h:10-808
AT5G49190.1 AT1G73370.1 932.2 807 942 802 803
802 803 q:5-806 h:11-813
AT5G49190.1 AT1G73370.2 917.5 807 898 768 769
768 769 q:39-806 h:1-769
AT5G49190.1 AT5G37180.1 895.2 807 836 791 788
791 788 q:15-805 h:14-801
AT5G49190.1 AT4G10120.1 164.1 807 1050 485 494
485 494 q:278-762 h:197-690
AT5G49190.1 AT4G10120.2 164.1 807 1050 485 494
485 494 q:278-762 h:197-690
AT5G49190.1 AT5G11110.1 159.1 807 1047 496 504
496 504 q:278-773 h:177-680
AT5G49190.1 AT1G04920.1 151.8 807 1062 485 500
485 500 q:278-762 h:172-671
AT5G49190.1 AT5G20280.1 145.6 807 1043 494 507
494 507 q:278-771 h:170-676
AT5G49190.1 AT1G78800.1 60.8 807 403 188 177
188 177 q:573-760 h:213-389
AT1G04920.1 AT5G49190.1 151.8 1062 807 500 485
500 485 q:172-671 h:278-762
AT1G73370.2 AT5G49190.1 917.5 898 807 769 768
769 768 q:1-769 h:39-806
AT5G11110.1 AT5G49190.1 159.1 1047 807 504 496
504 496 q:177-680 h:278-773
AT5G20280.1 AT5G49190.1 149.4 1043 807 507 494
507 494 q:170-676 h:278-771
AT5G20830.1 AT5G49190.1 1139.8 808 807 799 802
799 802 q:10-808 h:5-806
AT3G43190.1 AT5G49190.1 1152.1 808 807 799 802
799 802 q:10-808 h:5-806
[elserj at waterman ]$ cat
Arabidopsis_thaliana_phytozome_mart_9_9_13.fa-Oryza_sativa.japonica.IRGSP_gramene_ftp_1_17_14.fa
| grep AT5G49190
AT5G49190.1 OS03T0340500-01 1285.0 807 809 802 800
802 800 q:5-806 h:8-807
AT5G49190.1 OS06T0194900-03 1183.7 807 808 802 797
802 797 q:4-805 h:6-802
AT5G49190.1 OS06T0194900-02 1183.7 807 808 802 797
802 797 q:4-805 h:6-802
AT5G49190.1 OS06T0194900-01 1183.7 807 808 802 797
802 797 q:4-805 h:6-802
AT5G49190.1 OS03T0401300-01 1170.6 807 816 801 799
801 799 q:5-805 h:12-810
AT5G49190.1 OS07T0616800-01 1162.9 807 816 801 799
801 799 q:5-805 h:12-810
AT5G49190.1 OS06T0194900-04 992.6 807 649 644 643
644 643 q:162-805 h:1-643
AT5G49190.1 OS04T0309600-01 921.0 807 844 803 794
803 794 q:5-807 h:9-802
AT5G49190.1 OS04T0249500-00 920.2 807 844 802 793
802 793 q:5-806 h:9-801
AT5G49190.1 OS02T0831500-01 913.7 807 846 797 798
797 798 q:5-801 h:7-804
AT5G49190.1 OS03T0401300-02 481.5 807 315 310 309
310 309 q:496-805 h:1-309
AT5G49190.1 OS03T0340500-03 449.9 807 278 276 276
276 276 q:531-806 h:1-276
AT5G49190.1 OS03T0401300-03 203.8 807 132 126 126
126 126 q:680-805 h:1-126
AT5G49190.1 OS08T0301500-01 162.9 807 1066 494 507
494 507 q:278-771 h:188-694
AT5G49190.1 OS02T0184400-03 150.2 807 963 506 524
506 524 q:259-764 h:133-656
AT5G49190.1 OS02T0184400-02 150.2 807 963 506 524
506 524 q:259-764 h:133-656
AT5G49190.1 OS02T0184400-01 150.2 807 1011 506 524
506 524 q:259-764 h:181-704
AT5G49190.1 OS02T0184400-04 111.7 807 595 293 288
293 288 q:472-764 h:1-288
AT5G49190.1 OS11T0236100-01 84.0 807 509 143 135
143 135 q:630-772 h:4-138
[elserj at waterman ]$ cat
Oryza_sativa.japonica.IRGSP_gramene_ftp_1_17_14.fa-Arabidopsis_thaliana_phytozome_mart_9_9_13.fa
| grep AT5G49190
OS02T0184400-01 AT5G49190.1 150.2 1011 807 524 506
524 506 q:181-704 h:259-764
OS02T0184400-02 AT5G49190.1 150.2 963 807 524 506
524 506 q:133-656 h:259-764
OS02T0184400-03 AT5G49190.1 150.2 963 807 524 506
524 506 q:133-656 h:259-764
OS02T0184400-04 AT5G49190.1 111.7 595 807 288 293
288 293 q:1-288 h:472-764
OS02T0831500-01 AT5G49190.1 913.7 846 807 798 797
798 797 q:7-804 h:5-801
OS03T0340500-01 AT5G49190.1 1285.0 809 807 800 802
800 802 q:8-807 h:5-806
OS03T0340500-03 AT5G49190.1 449.9 278 807 276 276
276 276 q:1-276 h:531-806
OS03T0401300-01 AT5G49190.1 1170.6 816 807 799 801
799 801 q:12-810 h:5-805
OS03T0401300-02 AT5G49190.1 481.5 315 807 309 310
309 310 q:1-309 h:496-805
OS03T0401300-03 AT5G49190.1 203.8 132 807 126 126
126 126 q:1-126 h:680-805
OS04T0249500-00 AT5G49190.1 920.2 844 807 793 802
793 802 q:9-801 h:5-806
OS04T0309600-01 AT5G49190.1 921.0 844 807 794 803
794 803 q:9-802 h:5-807
OS06T0194900-01 AT5G49190.1 1183.7 808 807 797 802
797 802 q:6-802 h:4-805
OS06T0194900-02 AT5G49190.1 1183.7 808 807 797 802
797 802 q:6-802 h:4-805
OS06T0194900-03 AT5G49190.1 1183.7 808 807 797 802
797 802 q:6-802 h:4-805
OS06T0194900-04 AT5G49190.1 992.6 649 807 643 644
643 644 q:1-643 h:162-805
OS07T0616800-01 AT5G49190.1 1162.9 816 807 799 801
799 801 q:12-810 h:5-805
OS08T0301500-01 AT5G49190.1 162.2 1066 807 507 494
507 494 q:188-694 h:278-771
OS11T0236100-01 AT5G49190.1 83.2 509 807 135 143
135 143 q:4-138 h:630-772
--
**********************************************************
* *
* Justin Elser *
* Computational Biology Post Doc *
* Dept. of Botany and Plant Pathology *
* Oregon State University *
* *
* email: elserj at science.oregonstate.edu *
* internet: www.science.oregonstate.edu/~elserj *
* *
**********************************************************
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