From 87e164affe345f81758ecaa6289b8f3351e859d8 Mon Sep 17 00:00:00 2001 From: Brandon King Date: Tue, 23 May 2006 18:06:31 +0000 Subject: [PATCH] Conservation tracks + IUPAC Neucleotide Table * Added information about conservation tracks, and the meaning of blue vs red track. * Added an IUPAC Neucleotide Table --- doc/manual/images/conservation_tracks.png | Bin 3032 -> 3508 bytes doc/manual/mussagl_manual.rst | 62 +++++++++++++++++++--- 2 files changed, 55 insertions(+), 7 deletions(-) diff --git a/doc/manual/images/conservation_tracks.png b/doc/manual/images/conservation_tracks.png index 999c44fe400c056ec6f0584f49dfd37762092ad9..6c001c5d12dd81df932c19d5935d60ba0acde4d4 100644 GIT binary patch literal 3508 zcmV;l4NLNgP)v%jKVcK#40I0U-IN3KiQ9C>@13Y^s^ZQ1?`X(PEsWJgC8*`TuB|>;3TL7$fOAK%Bm_wrZG`X)AiLs9 zp_>?`yV4!o*?$+#bP^k!HI(UCZJRA8nkF5Lfi}_ZUBk6mu1aRglokVR()B?lT&vn_ zb(~oR1ZRpVRTq}A*+@7u>=*h+LZY8rEz6ow;d`st;T*xOhieU+je#?dUgOMATghho zkQ7NXY$?qfZ9+1-1@vO+P-)&NYB+SDsX?33W^2Tm2c@~9t((|LL7SKN&fTZtEJi?Z z#8~r!HjB-6nWQ|PiqUa&i0EZZW6$JDGtafe+94~a3wq|NDg3WfP`!1Zt zQ%`ShqlKeAQ5%E_C2=-L$I&{pW}yrG82*l`UYy0Iv`;%R=A@UL-(eoZ=g6!#TNo#+ zHAh=5G*i|DS~wem(oW-wrolFws9|h2VbL6PQa)R2t)#^O^#(AK&6cDtF)|txY9`!9 z80@h$!5L>GM(RC1FicBy2Ha3alSq(+$A~HIZ~xI~re{JfnW#C9L@wVK#@Wb}=2w$y zBgD{VD~P5fHpZniHwWYvFUc61+iV5V6vo-Ol$Hu3+5;ShHPtLcbB-)6(|GiPzB;}| z>w_GgwAg1*sC|}6Wg3s_Ja8HfI}VVu*&J{-MM2=2w+(1X=8`Z)JdE#g6vW{HO3xB* zykZeXA)BoLCS9COKxsv&nLJDQoV^m8FpmQsnfs~jpE(hw)lyy~B{hm$8zheI zP{-Nm1pyJ0@DdGF9eCZdSGwzipZR&1E89#3!R?pd&VB4RP*&2Ikt{Qo5eDW^&nnbT zyrZC`E^pD1Wi*SkT79r7jjf)KL|`?!P5iCzO=CBuHBFD3Zrsl+dTOY$1L8$&m(FJjmDDMSo6_3lp#H?=5OqMFED|nC2d_lf zP-|#&0&15$SoXbyms#vxA6yTHETj}RP?)$N_z2~Z3F#?alYB2BaU`R;j6OS5NzNW| z>0uc4B$x2tbPa^wOZcHm*DH4dsTg;9t)ZMEuhEBzDXseP zlZGbCFBAwV^?VzdxV$L(OlH3}o1Lk#6s1+?@UP_|wo=?>_Fge`dwyVTYOF_T6uG!q z9=&L*L{;HX+X{vr4>*n%S`oy@>>kJ4cBmb@lh@D|v}KQJSJ(i7XpB{&u+>uxYDeYa z)ra{+-b<*QC}lZ{#y!E95RbqWF+)T%MTt`>^c2Ng0q+li2_4>qNVQ(6UTh0-nc zF^n*Q>7HV}OS>QtnjWNRpGAgHoS~R{HVpv7yS`VWE_*jGP!Rn5#UYTceMSv?8`-2~ z^a>!GoNe_~RZj}kp8qAJYoD89ZzK8JH`7HE?n^nm_HJHHJqumFXv>S(NC?5k*j|he zLYLUdS-CZ4dpEB^X#kv)bXgjDq7Ce7Cwbq=Mw|^eW+PHsqN9Zus|Zi1a*e^3cG5_N z-s_g{)vga#qO`i0+&;vuSg#HUyPbI%mBg9L-pwmf8n8~Wrahs`nHAU`-qdCvbTcF_ zcdX%YWdEqJwFlqwxcn_b!+DH1Vq-z4{S?GAv1!QYGU`c!T28q5>DqVgZs$zqiYA0T zI(Vz+oyL+S0>|>W=56d%I=?>{iKc3Ouqmzjp;pV|a<`_{l<;`1(r(%fxhpW@^}#Zf z2G!?~xw7wMd9=)*x!g=wg({ zvpGuX8qe~${EUoN9)@J0Dx=GI96)>sDYwcar=cZoOZ&_D@pcoX{m@ezYOHiEuc3+O zqzsedWV3r^pzLi*H0pCI?1E=sVS}gr?qpaem+atp*#QBAQ61} zj#^(wcPx4s?&?raAg-pNY&Ut?4~saTYkc`f&(W=^qDMwQ|97mzj`|Wc_QEYg4J|n! 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By default all 10 motifs start off as with white as the color. + +.. image:: images/motif_dialog_start.png + :alt: Motif Dialog + :align: center + Detailed Info ------------- @@ -583,6 +600,37 @@ Example: GGCC 0.0 1 1 + +IUPAC Nucleotide Code +~~~~~~~~~~~~~~~~~~~~~ + +For your convience, below is a table of the IUPAC Nucleotide Code. + +The following table is table 1 from "Nomenclature for Incompletely +Specified Bases in Nucleic Acid Sequences" which can be found at +http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html. + +====== ================= =================================== +Symbol Meaning Origin of designation +====== ================= =================================== +G G Guanine +A A Adenine +T T Thymine +C C Cytosine +R G or A puRine +Y T or C pYrimidine +M A or C aMino +K G or T Keto +S G or C Strong interaction (3 H bonds) +W A or T Weak interaction (2 H bonds) +H A or C or T not-G, H follows G in the alphabet +B G or T or C not-A, B follows A +V G or C or A not-T (not-U), V follows U +D G or A or T not-C, D follows C +N G or A or T or C aNy +====== ================= =================================== + + .. Define links below ------------------ -- 2.30.2