First commit with program and example codon usage tables.

tdseher · Feb 20, 2019 · aa9b71a · aa9b71a
1 parent c6ced06
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diff --git a/examples/5501_codons.txt b/examples/5501_codons.txt
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+id,value
+taxid,5501
+collapse,4
+"#codon",17277496
+"#CDS",39640
+"GC%",50.78
+"GC1%",55.85
+"GC2%",44.36
+"GC3%",52.13
+TTT,291368
+TTC,349064
+TTA,140536
+TTG,281524
+CTT,337452
+CTC,343944
+CTA,163988
+CTG,278148
+ATT,329656
+ATC,377884
+ATA,168296
+ATG,368400
+GTT,313632
+GTC,314600
+GTA,121956
+GTG,258528
+TAT,237604
+TAC,222076
+TAA,13436
+TAG,9092
+CAT,232416
+CAC,190644
+CAA,326356
+CAG,370060
+AAT,331276
+AAC,319832
+AAA,402628
+AAG,481472
+GAT,531948
+GAC,419976
+GAA,560712
+GAG,524856
+TCT,287384
+TCC,298932
+TCA,230612
+TCG,229684
+CCT,283644
+CCC,248512
+CCA,306240
+CCG,240160
+ACT,235828
+ACC,289932
+ACA,244556
+ACG,206384
+GCT,381676
+GCC,381452
+GCA,338976
+GCG,282004
+TGT,94896
+TGC,131700
+TGA,17112
+TGG,234756
+CGT,168068
+CGC,215888
+CGA,210676
+CGG,167304
+AGT,172268
+AGC,264248
+AGA,208276
+AGG,157392
+GGT,272268
+GGC,347092
+GGA,315272
+GGG,200944
diff --git a/examples/Codon usage table 5501.html b/examples/Codon usage table 5501.html
@@ -0,0 +1,123 @@
+<HTML>
+<HEAD>
+<META HTTP-EQUIV="Content-Type" CONTENT="text/html; charset=iso-8859-1">
+<TITLE>Codon usage table</TITLE>
+</HEAD>
+
+<BODY BGCOLOR="#F0F0F0">
+<STRONG><i>Coccidioides immitis </i>[gbpln]: 30 CDS's (13160 codons)</STRONG>
+
+<HR ALIGN="LEFT" SIZE=1>
+
+fields: [triplet] [frequency: <STRONG>per thousand</STRONG>] ([number])
+<HR ALIGN="LEFT" SIZE=1>
+<PRE>
+UUU 15.3(   201)  UCU 15.7(   207)  UAU 15.0(   198)  UGU  6.2(    82)
+UUC 24.8(   327)  UCC 15.6(   205)  UAC 16.5(   217)  UGC  7.7(   101)
+UUA  4.7(    62)  UCA  7.8(   102)  UAA  0.9(    12)  UGA  1.0(    13)
+UUG 16.5(   217)  UCG 10.9(   144)  UAG  0.4(     5)  UGG 12.5(   164)
+
+CUU 17.8(   234)  CCU 13.7(   180)  CAU  8.3(   109)  CGU 12.4(   163)
+CUC 22.6(   297)  CCC 14.4(   189)  CAC 13.0(   171)  CGC 17.4(   229)
+CUA  7.0(    92)  CCA 18.5(   243)  CAA 14.4(   189)  CGA  8.8(   116)
+CUG 14.2(   187)  CCG 10.6(   139)  CAG 22.1(   291)  CGG  6.5(    85)
+
+AUU 19.8(   261)  ACU 15.5(   204)  AAU 18.5(   243)  AGU  6.9(    91)
+AUC 27.6(   363)  ACC 22.0(   290)  AAC 27.5(   362)  AGC 14.5(   191)
+AUA  6.1(    80)  ACA 13.4(   177)  AAA 21.1(   278)  AGA  8.7(   114)
+AUG 21.6(   284)  ACG 10.6(   140)  AAG 34.7(   457)  AGG  4.9(    65)
+
+GUU 21.4(   281)  GCU 22.6(   298)  GAU 29.9(   394)  GGU 20.0(   263)
+GUC 23.3(   306)  GCC 27.5(   362)  GAC 28.0(   369)  GGC 22.0(   290)
+GUA  5.0(    66)  GCA 16.3(   214)  GAA 31.5(   415)  GGA 16.4(   216)
+GUG 14.1(   186)  GCG 12.8(   168)  GAG 34.0(   448)  GGG  8.6(   113)
+</PRE>
+<HR ALIGN="LEFT" SIZE=1>
+Coding GC 51.22%
+1st letter GC 55.49%
+2nd letter GC 42.23%
+3rd letter GC 55.94%<BR>
+
+
+<HR ALIGN="LEFT" SIZE=1>
+
+<FORM ACTION="./showcodon.cgi" METHOD="GET">
+
+<STRONG>Format:</STRONG><BR>
+
+<!-- INPUT TYPE="HIDDEN" NAME="species" VALUE="Coccidioides immitis [gbpln]" -->
+<INPUT TYPE="HIDDEN" NAME="species" VALUE="5501">
+
+<SELECT NAME="aa">
+<OPTION SELECTED>SELECT A CODE
+<OPTION VALUE="1">1: Standard
+<OPTION VALUE="2">2: Vertebrate Mitochondrial
+<OPTION VALUE="3">3: Yeast Mitochondrial
+<OPTION VALUE="4">4: Mold, Protozoan, Coelenterate Mitochondrial
+<OPTION VALUE="4">(4:)	and Mycoplasma/Spiroplasma
+<OPTION VALUE="5">5: Invertebrate Mitochondrial
+<OPTION VALUE="6">6: Ciliate Macronuclear and Dasycladacean
+<OPTION VALUE="9">9: Echinoderm Mitochondrial
+<OPTION VALUE="10">10: Alternative Ciliate Macronuclear
+<OPTION VALUE="11">11: Eubacterial
+<OPTION VALUE="12">12: Alternative Yeast
+<OPTION VALUE="13">13: Ascidian Mitochondrial
+<OPTION VALUE="14">14: Flatworm Mitochondrial
+<OPTION VALUE="15">15: Blepharisma Nuclear Code
+</SELECT>
+
+<A HREF = "http://www3.ncbi.nlm.nih.gov/htbin-post/Taxonomy/wprintgc?mode=t">
+Genetic codes (NCBI)</A>
+
+<BR>
+
+<INPUT TYPE="radio" NAME="style" VALUE="N" CHECKED>
+<!-- INPUT TYPE="hidden" NAME="style" VALUE="N" -->
+Codon Usage Table with Amino Acids
+<BR>
+
+<INPUT TYPE="radio" NAME="style" VALUE="GCG">
+A style like CodonFrequency output in GCG <A HREF="http://www.gcg.com/products/software.html">Wisconsin Package<SUP>TM</SUP></A>
+
+<BR>
+
+<!-- INPUT TYPE="radio" NAME="style" VALUE="BT")Back translation (comming soon)
+(BR)
+(TEXTAREA NAME="aa_src" ROWS="2" COLS="60")(/TEXTAREA)
+(P -->
+<INPUT TYPE=SUBMIT VALUE="Submit">
+</FORM>
+
+<HR ALIGN="LEFT" SIZE=1>
+
+<FORM ACTION="srchcds.cgi" METHOD="POST">
+
+<STRONG>CDS Search:</STRONG><BR>
+
+<INPUT SIZE="40" TYPE="TEXT" NAME="key">
+<INPUT TYPE=SUBMIT VALUE="Submit">
+
+<INPUT TYPE="HIDDEN" NAME="abbrev" VALUE="5501">
+<INPUT TYPE="HIDDEN" NAME="entry" VALUE="pln">
+<INPUT TYPE="HIDDEN" NAME="sponly" VALUE="Coccidioides immitis">
+
+<BR>
+
+Keyword example: ribosomal protein / MAP kinase
+
+</FORM>
+
+<!-- A HREF="ftp://ftp.kazusa.or.jp/pub/codon/current/species/5501.pln" -->
+<A HREF="http://www.kazusa.or.jp/codon/current/species/5501">
+List of codon usage for each CDS 
+</A> 
+<A HREF="http://www.kazusa.or.jp/codon/current/CODON_LABEL">
+(format)
+</A>
+
+<HR ALIGN="LEFT" SIZE=1>
+
+<I><A HREF= "/codon/">Homepage</A></I>
+
+</BODY>
+</HTML>
diff --git a/examples/o569942-refseq-GCF_000149335.2.txt b/examples/o569942-refseq-GCF_000149335.2.txt
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+Division	Assembly	Taxid	Species	Organelle	Translation Table	# CDS	# Codons	GC%	GC1%	GC2%	GC3%	TTT	TTC	TTA	TTG	CTT	CTC	CTA	CTG	ATT	ATC	ATA	ATG	GTT	GTC	GTA	GTG	TAT	TAC	TAA	TAG	CAT	CAC	CAA	CAG	AAT	AAC	AAA	AAG	GAT	GAC	GAA	GAG	TCT	TCC	TCA	TCG	CCT	CCC	CCA	CCG	ACT	ACC	ACA	ACG	GCT	GCC	GCA	GCG	TGT	TGC	TGA	TGG	CGT	CGC	CGA	CGG	AGT	AGC	AGA	AGG	GGT	GGC	GGA	GGG
+refseq	GCF_000149335.2	246410	Coccidioides immitis RS	genomic	1	9910	4319374	50.78	55.85	44.36	52.13	72842	87266	35134	70381	84363	85986	40997	69537	82414	94471	42074	92100	78408	78650	30489	64632	59401	55519	3359	2273	58104	47661	81589	92515	82819	79958	100657	120368	132987	104994	140178	131214	71846	74733	57653	57421	70911	62128	76560	60040	58957	72483	61139	51596	95419	95363	84744	70501	23724	32925	4278	58689	42017	53972	52669	41826	43067	66062	52069	39348	68067	86773	78818	50236
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		Division Assembly Taxid Species Organelle Translation Table # CDS # Codons GC% GC1% GC2% GC3% TTT TTC TTA TTG CTT CTC CTA CTG ATT ATC ATA ATG GTT GTC GTA GTG TAT TAC TAA TAG CAT CAC CAA CAG AAT AAC AAA AAG GAT GAC GAA GAG TCT TCC TCA TCG CCT CCC CCA CCG ACT ACC ACA ACG GCT GCC GCA GCG TGT TGC TGA TGG CGT CGC CGA CGG AGT AGC AGA AGG GGT GGC GGA GGG
		refseq GCF_000149335.2 246410 Coccidioides immitis RS genomic 1 9910 4319374 50.78 55.85 44.36 52.13 72842 87266 35134 70381 84363 85986 40997 69537 82414 94471 42074 92100 78408 78650 30489 64632 59401 55519 3359 2273 58104 47661 81589 92515 82819 79958 100657 120368 132987 104994 140178 131214 71846 74733 57653 57421 70911 62128 76560 60040 58957 72483 61139 51596 95419 95363 84744 70501 23724 32925 4278 58689 42017 53972 52669 41826 43067 66062 52069 39348 68067 86773 78818 50236