squizz(1) [debian man page]

SQUIZZ(1)							   User Manuals 							 SQUIZZ(1)

NAME

       squizz - Sequence format checker

SYNOPSIS

       squizz [-AShlns] [-c format] [-f format] file

OPTIONS

       Following command line options are allowed:

       -A  Restrict detection/verification to alignment formats (conflict with -S option).

       -S  Restrict detection/verification to sequence formats (conflict with -A option).

       -c format
	   Convert detected sequence/alignment into format. This option implies strict alignment checking.

       -f format
	   Assume input format is format. Do not try to detect the format, just verify that the given one is correct.

       -h  Usage display.

       -l  List all supported formats.

       -n  Count and report detected entries. This option is only available when the detection is restricted to a single type (with -A or -S
	   options) and strict checks (without -s option) are enabled.

       -s  Disable strict format checks (enabled by default).

DESCRIPTION

       squizz is a sequence format file checker, but it has some conversion capabilities too.

       squizz can detect the most common sequence and alignment formats :

       * EMBL, FASTA, GCG, GDE, GENBANK, IG, NBRF, PIR (codata), RAW, and SWISSPROT.

       * CLUSTAL, FASTA, MSF, NEXUS, PHYLIP (interleaved and sequential) and STOCKHOLM.

       squizz can do some conversions too, if the format the input format is supported. Only 3 types are available : sequence to sequence, align-
       ment to alignment, and alignment to sequence (the last one, sequence to alignment, require multiple alignments algorithms and cannot be
       handled with formatting tools).

       Strict format checks validate the previously detected objects, by making some sanity checks:

       - sequence strings must exists.
       - alignment is made of more than one sequence.
       - alignment sequence strings must have the same length.
       - alignment sequence names must exists, and be unique.

SEE ALSO

       seqfmt(5), alifmt(5)

AUTHOR

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

Unix								    2009-05-19								 SQUIZZ(1)

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)