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PMC:441373 / 47559-48295 JSONTXT

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craft-sa-dev

Id Subject Object Predicate Lexical cue
T11820 0-5 DT denotes These
T11821 14-23 NNS denotes sequences
T11822 6-13 NN denotes protein
T11823 39-46 VBN denotes aligned
T11824 24-28 VBD denotes were
T11825 29-38 RB denotes initially
T11826 47-51 IN denotes with
T11827 52-59 NNP denotes CLUSTAL
T11828 60-61 NNP denotes X
T11829 62-63 -LRB- denotes [
T11830 63-65 CD denotes 38
T11831 65-66 -RRB- denotes ]
T11832 66-67 . denotes .
T11833 67-403 sentence denotes Minor adjustments to certain regions of the alignment for optimization purposes were made based on pairwise alignments, the output saved in PHYLIP format, after which, the distances between proteins were calculated using Poisson correction and the Unrooted trees were inferred with the NJ method and then displayed using TreeView [39].
T11834 68-73 JJ denotes Minor
T11835 74-85 NNS denotes adjustments
T11836 153-157 VBN denotes made
T11837 86-88 IN denotes to
T11838 89-96 JJ denotes certain
T11839 97-104 NNS denotes regions
T11840 105-107 IN denotes of
T11841 108-111 DT denotes the
T11842 112-121 NN denotes alignment
T11843 122-125 IN denotes for
T11844 126-138 NN denotes optimization
T11845 139-147 NNS denotes purposes
T11846 148-152 VBD denotes were
T11847 199-204 VBD denotes saved
T11848 158-163 VBN denotes based
T11849 164-166 IN denotes on
T11850 167-175 JJ denotes pairwise
T11851 176-186 NNS denotes alignments
T11852 186-188 , denotes ,
T11853 188-191 DT denotes the
T11854 192-198 NN denotes output
T11855 205-207 IN denotes in
T11856 208-214 NN denotes PHYLIP
T11857 215-221 NN denotes format
T11858 221-223 , denotes ,
T11859 223-228 IN denotes after
T11860 272-282 VBN denotes calculated
T11861 229-234 WDT denotes which
T11862 234-236 , denotes ,
T11863 236-239 DT denotes the
T11864 240-249 NNS denotes distances
T11865 250-257 IN denotes between
T11866 258-266 NN denotes proteins
T11867 267-271 VBD denotes were
T11868 283-288 VBG denotes using
T11869 289-296 NNP denotes Poisson
T11870 297-307 NN denotes correction
T11871 308-311 CC denotes and
T11872 312-315 DT denotes the
T11873 325-330 NNS denotes trees
T11874 316-324 JJ denotes Unrooted
T11875 336-344 VBN denotes inferred
T11876 331-335 VBD denotes were
T11877 345-349 IN denotes with
T11878 350-353 DT denotes the
T11879 357-363 NN denotes method
T11880 354-356 NN denotes NJ
T11881 364-367 CC denotes and
T11882 368-372 RB denotes then
T11883 373-382 VBD denotes displayed
T11884 383-388 VBG denotes using
T11885 389-397 NNP denotes TreeView
T11886 398-399 -LRB- denotes [
T11887 399-401 CD denotes 39
T11888 401-402 -RRB- denotes ]
T11889 402-403 . denotes .
T11890 403-469 sentence denotes Bootstrap values above 700 for 1000 trials are shown at the node.
T11891 404-413 NN denotes Bootstrap
T11892 414-420 NNS denotes values
T11893 451-456 VBN denotes shown
T11894 421-426 IN denotes above
T11895 427-430 CD denotes 700
T11896 431-434 IN denotes for
T11897 435-439 CD denotes 1000
T11898 440-446 NNS denotes trials
T11899 447-450 VBP denotes are
T11900 457-459 IN denotes at
T11901 460-463 DT denotes the
T11902 464-468 NN denotes node
T11903 468-469 . denotes .
T11904 469-645 sentence denotes To validate the tree, the same sequence set was analyzed with tools in the PHYLIP package [40], using PRODIST followed by FITCH or NEIGNBOR and tree displaying using TreeView.
T11905 470-472 TO denotes To
T11906 473-481 VB denotes validate
T11907 518-526 VBN denotes analyzed
T11908 482-485 DT denotes the
T11909 486-490 NN denotes tree
T11910 490-492 , denotes ,
T11911 492-495 DT denotes the
T11912 510-513 NN denotes set
T11913 496-500 JJ denotes same
T11914 501-509 NN denotes sequence
T11915 514-517 VBD denotes was
T11916 527-531 IN denotes with
T11917 532-537 NNS denotes tools
T11918 538-540 IN denotes in
T11919 541-544 DT denotes the
T11920 552-559 NN denotes package
T11921 545-551 NN denotes PHYLIP
T11922 560-561 -LRB- denotes [
T11923 561-563 CD denotes 40
T11924 563-564 -RRB- denotes ]
T11925 564-566 , denotes ,
T11926 566-571 VBG denotes using
T11927 572-579 NN denotes PRODIST
T11928 580-588 VBN denotes followed
T11929 589-591 IN denotes by
T11930 592-597 NN denotes FITCH
T11931 598-600 CC denotes or
T11932 601-609 NN denotes NEIGNBOR
T11933 610-613 CC denotes and
T11934 614-618 NN denotes tree
T11935 619-629 VBG denotes displaying
T11936 630-635 VBG denotes using
T11937 636-644 NNP denotes TreeView
T11938 644-645 . denotes .
T11939 645-736 sentence denotes This additional method produced trees with essentially the same topology (data not shown).
T11940 646-650 DT denotes This
T11941 662-668 NN denotes method
T11942 651-661 JJ denotes additional
T11943 669-677 VBD denotes produced
T11944 678-683 NNS denotes trees
T11945 684-688 IN denotes with
T11946 689-700 RB denotes essentially
T11947 710-718 NN denotes topology
T11948 701-704 DT denotes the
T11949 705-709 JJ denotes same
T11950 719-720 -LRB- denotes (
T11951 729-734 VBN denotes shown
T11952 720-724 NNS denotes data
T11953 725-728 RB denotes not
T11954 734-735 -RRB- denotes )
T11955 735-736 . denotes .
R7647 T11820 T11821 det These,sequences
R7648 T11821 T11823 nsubjpass sequences,aligned
R7649 T11822 T11821 compound protein,sequences
R7650 T11824 T11823 auxpass were,aligned
R7651 T11825 T11823 advmod initially,aligned
R7652 T11826 T11823 prep with,aligned
R7653 T11827 T11828 compound CLUSTAL,X
R7654 T11828 T11826 pobj X,with
R7655 T11829 T11830 punct [,38
R7656 T11830 T11823 parataxis 38,aligned
R7657 T11831 T11830 punct ],38
R7658 T11832 T11823 punct .,aligned
R7659 T11834 T11835 amod Minor,adjustments
R7660 T11835 T11836 nsubjpass adjustments,made
R7661 T11836 T11847 ccomp made,saved
R7662 T11837 T11835 prep to,adjustments
R7663 T11838 T11839 amod certain,regions
R7664 T11839 T11837 pobj regions,to
R7665 T11840 T11839 prep of,regions
R7666 T11841 T11842 det the,alignment
R7667 T11842 T11840 pobj alignment,of
R7668 T11843 T11835 prep for,adjustments
R7669 T11844 T11845 compound optimization,purposes
R7670 T11845 T11843 pobj purposes,for
R7671 T11846 T11836 auxpass were,made
R7672 T11848 T11836 prep based,made
R7673 T11849 T11848 prep on,based
R7674 T11850 T11851 amod pairwise,alignments
R7675 T11851 T11849 pobj alignments,on
R7676 T11852 T11847 punct ", ",saved
R7677 T11853 T11854 det the,output
R7678 T11854 T11847 nsubj output,saved
R7679 T11855 T11847 prep in,saved
R7680 T11856 T11857 compound PHYLIP,format
R7681 T11857 T11855 pobj format,in
R7682 T11858 T11847 punct ", ",saved
R7683 T11859 T11860 prep after,calculated
R7684 T11860 T11847 advcl calculated,saved
R7685 T11861 T11859 pobj which,after
R7686 T11862 T11860 punct ", ",calculated
R7687 T11863 T11864 det the,distances
R7688 T11864 T11860 nsubjpass distances,calculated
R7689 T11865 T11864 prep between,distances
R7690 T11866 T11865 pobj proteins,between
R7691 T11867 T11860 auxpass were,calculated
R7692 T11868 T11860 advcl using,calculated
R7693 T11869 T11870 compound Poisson,correction
R7694 T11870 T11868 dobj correction,using
R7695 T11871 T11860 cc and,calculated
R7696 T11872 T11873 det the,trees
R7697 T11873 T11875 nsubjpass trees,inferred
R7698 T11874 T11873 amod Unrooted,trees
R7699 T11875 T11860 conj inferred,calculated
R7700 T11876 T11875 auxpass were,inferred
R7701 T11877 T11875 prep with,inferred
R7702 T11878 T11879 det the,method
R7703 T11879 T11877 pobj method,with
R7704 T11880 T11879 compound NJ,method
R7705 T11881 T11875 cc and,inferred
R7706 T11882 T11883 advmod then,displayed
R7707 T11883 T11875 conj displayed,inferred
R7708 T11884 T11883 advcl using,displayed
R7709 T11885 T11884 dobj TreeView,using
R7710 T11886 T11887 punct [,39
R7711 T11887 T11883 parataxis 39,displayed
R7712 T11888 T11887 punct ],39
R7713 T11889 T11847 punct .,saved
R7714 T11891 T11892 compound Bootstrap,values
R7715 T11892 T11893 nsubjpass values,shown
R7716 T11894 T11892 prep above,values
R7717 T11895 T11894 pobj 700,above
R7718 T11896 T11892 prep for,values
R7719 T11897 T11898 nummod 1000,trials
R7720 T11898 T11896 pobj trials,for
R7721 T11899 T11893 auxpass are,shown
R7722 T11900 T11893 prep at,shown
R7723 T11901 T11902 det the,node
R7724 T11902 T11900 pobj node,at
R7725 T11903 T11893 punct .,shown
R7726 T11905 T11906 aux To,validate
R7727 T11906 T11907 advcl validate,analyzed
R7728 T11908 T11909 det the,tree
R7729 T11909 T11906 dobj tree,validate
R7730 T11910 T11907 punct ", ",analyzed
R7731 T11911 T11912 det the,set
R7732 T11912 T11907 nsubjpass set,analyzed
R7733 T11913 T11912 amod same,set
R7734 T11914 T11912 compound sequence,set
R7735 T11915 T11907 auxpass was,analyzed
R7736 T11916 T11907 prep with,analyzed
R7737 T11917 T11916 pobj tools,with
R7738 T11918 T11917 prep in,tools
R7739 T11919 T11920 det the,package
R7740 T11920 T11918 pobj package,in
R7741 T11921 T11920 compound PHYLIP,package
R7742 T11922 T11923 punct [,40
R7743 T11923 T11907 parataxis 40,analyzed
R7744 T11924 T11923 punct ],40
R7745 T11925 T11907 punct ", ",analyzed
R7746 T11926 T11907 advcl using,analyzed
R7747 T11927 T11926 dobj PRODIST,using
R7748 T11928 T11927 acl followed,PRODIST
R7749 T11929 T11928 agent by,followed
R7750 T11930 T11929 pobj FITCH,by
R7751 T11931 T11930 cc or,FITCH
R7752 T11932 T11930 conj NEIGNBOR,FITCH
R7753 T11933 T11926 cc and,using
R7754 T11934 T11935 dep tree,displaying
R7755 T11935 T11926 conj displaying,using
R7756 T11936 T11935 advcl using,displaying
R7757 T11937 T11936 dobj TreeView,using
R7758 T11938 T11907 punct .,analyzed
R7759 T11940 T11941 det This,method
R7760 T11941 T11943 nsubj method,produced
R7761 T11942 T11941 amod additional,method
R7762 T11944 T11943 dobj trees,produced
R7763 T11945 T11944 prep with,trees
R7764 T11946 T11947 advmod essentially,topology
R7765 T11947 T11945 pobj topology,with
R7766 T11948 T11947 det the,topology
R7767 T11949 T11947 amod same,topology
R7768 T11950 T11951 punct (,shown
R7769 T11951 T11943 parataxis shown,produced
R7770 T11952 T11951 nsubj data,shown
R7771 T11953 T11951 neg not,shown
R7772 T11954 T11951 punct ),shown
R7773 T11955 T11943 punct .,produced

craft-ca-core-ex-dev

Below, discontinuous spans are shown in the chain model. You can change it to the bag model.

Id Subject Object Predicate Lexical cue
T11430 6-13 CHEBI_PR_EXT:protein denotes protein
T11431 14-23 SO_EXT:biological_sequence denotes sequences
T11432 258-266 CHEBI_PR_EXT:protein denotes proteins
T11433 501-509 SO_EXT:biological_sequence denotes sequence

2_test

Id Subject Object Predicate Lexical cue
15207008-9810230-9666077 63-65 9810230 denotes 38
15207008-8902363-9666078 399-401 8902363 denotes 39
15207008-3071258-9666079 561-563 3071258 denotes 40