Script to do column to row Post: 303043576

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LEARN ABOUT DEBIAN

seqfmt

SEQFMT(5)							   User Manuals 							 SEQFMT(5)

NAME

       seqfmt - Sequences formats

DESCRIPTION

       This document illustrates some common formats used for sequences representation.

       EMBL
	    ID	 MMVASPHOS  standard; RNA; EST; 140 BP.
	    AC	 X97897;
	    DE	 M.musculus mRNA for protein homologous to
	    DE	 vasodilator-stimulated phosphoprotein
	    SQ	 Sequence 140 BP; 25 A; 58 C; 39 G; 17 T; 1 other;
		 ttctcccaga agctgactct atggngaccc cgagagagac tgagcagaac      60
		 ccccgcaccc ctgcacttcc aatcaggggc gccccgggag cactccccgt     120
		 ccgccctccg cgcagccatg					    140
	    //

       FASTA
	    >MMVASPHOS
	    ttctcccagaagctgactctatggngaccccgagagagactgagcagaacctggagccag
	    ccccgcacccctgcacttccaatcaggggcgccccgggagcactccccgtggcgcgccgc
	    ccgccctccgcgcagccatg

       GCG
	    !!NA_SEQUENCE 1.0
	     (No documentation)
	    dna1.txt  Length: 88  Nov 22, 2001 14:38  Type: N  Check: 3818  ..

		   1  TAGTCGTAGT CGGAGCGATG CTGACGATGA CGATGACGAT CGTAGCTGAT

		  51  CGATCGAGCT GATGCTGATC GAGCTAGCTG ATCGATCG

       GDE
	    #sample1
	    TTCAAGAGAAACAGCGGCCAAGGAAAAGACTCGGCATGATTGTCCATAGCTTACAAAGCG
	    #sample2
	    TTCAAGAGAAACAGCGGCTGGGGGAAAGACTCGTCCTGATTGCCTGTAGATGGTAAAGCG

       GENBANK
	    LOCUS	HUMHBV1       130 bp	DNA	    PRI     17-JUN-1993
	    DEFINITION	Human DNA/endogenous Hepatitis B virus (HBV) DNA, left
			host viral junction.
	    ACCESSION	M15770
	    BASE COUNT	     32 a     43 c     29 g	26 t
	    ORIGIN
		  1 agcgggcagt gcagctgctt ggacagcagg ggtgtttctt caacccaggc
		 61 ctcctgtcac aacaggccca ttcaattctg aacctgcaag ccaactccaa
		121 cctcttttcc cagggggaac caaaaaccct
	    //

       IG
	    ; comment
	    U03518
	    AACCTGCGGAAGGATCATTACCGAGTGCGGGTCCTTTGGGCCCAACCTCCCATCCGTGTC
	    TATTGTACCCTGTTGCTTCGGCGGGCCCGCCGCTTGTCGGCCGCCGGGGGGGCGCCTCTG
	    TGAGTTGATTGAATGCAATCAGTTAAAACTTTCAACAATGGATCTCTTGGTTCCGGC1

       NBRF
	    >P1;CCHU
	    cytochrome c [validated] - human
	    MGDVEKGKKIFIMKCSQCHTVEKGGKHKTGPNLHGLFGRKTGQAPGYSYTAANKNKGIIW
	    GEDTLMEYLENPKKYIPGTKMIFVGIKKKEERADLIAYLKKATNE*

       PIR
	    ENTRY	   CCHU  #type complete
	    TITLE	   cytochrome c [validated] - human
	    ACCESSIONS	   A31764; A05676; I55192; A00001
	    SUMMARY	   #length 105	#molecular-weight 11749  #checksum 3247
	    SEQUENCE
			    5	     10        15	 20	   25	     30
		  1 M G D V E K G K K I F I M K C S Q C H T V E K G G K H K T G
		 31 P N L H G L F G R K T G Q A P G Y S Y T A A N K N K G I I W
		 61 G E D T L M E Y L E N P K K Y I P G T K M I F V G I K K K E
		 91 E R A D L I A Y L K K A T N E
	    ///

       RAW
	    ttctcccagaagctgactctatggngaccccgagagagactgagcagaacctggagccag
	    ccccgcacccctgcacttccaatcaggggcgccccgggagcactccccgtggcgcgccgc
	    ccgccctccgcgcagccatg

	   Warning: This format cannot handle more than one sequence per file.

       SWISSPROT
	    ID	 100K_RAT	STANDARD;      PRT;   149 AA.
	    AC	 Q62671;
	    DE	 100 kDa protein (EC 6.3.2.-).
	    SQ	 SEQUENCE   149 AA;  17004 MW;	D06484B8BC29112E CRC64;
		 MMSARGDFLN YALSLMRSHN DEHSDVLPVL DVCSLKHVAY VFQALIYWIK
		 PQLERKRTRE LLELGIDNED SEHENDDDTS QSATLNDKDD ESLPAETGQN
		 SITIRPPDDQ HLPTANTCIS RLYVPLYSSK QILKQKLLLA IKTKNFGFV
	    //

SEE ALSO

       squizz(1), alifmt(5)

AUTHOR

       Nicolas Joly (njoly@pasteur.fr), Institut Pasteur.

Unix								    2009-05-19								 SEQFMT(5)