Compare and report features of two similar sequences
Version: EMBOSS:6.4.0.0

   Standard (Mandatory) qualifiers:
  [-asequence]         sequence   Sequence filename and optional format, or
                                  reference (input USA)
  [-bsequence]         sequence   Sequence filename and optional format, or
                                  reference (input USA)
   -wordsize           integer    [10] The similar regions between the two
                                  sequences are found by creating a hash table
                                  of 'wordsize'd subsequences. 10 is a
                                  reasonable default. Making this value larger
                                  (20?) may speed up the program slightly,
                                  but will mean that any two differences
                                  within 'wordsize' of each other will be
                                  grouped as a single region of difference.
                                  This value may be made smaller (4?) to
                                  improve the resolution of nearby
                                  differences, but the program will go much
                                  slower. (Integer 2 or more)
  [-outfile]           report     [*.diffseq] Output report file name (default
                                  -rformat diffseq)
  [-aoutfeat]          featout    [$(asequence.name).diffgff] File for output
                                  of first sequence's features
  [-boutfeat]          featout    [$(bsequence.name).diffgff] File for output
                                  of second sequence's features

   Additional (Optional) qualifiers:
   -globaldifferences  boolean    [N] Normally this program will find regions
                                  of identity that are the length of the
                                  specified word-size or greater and will then
                                  report the regions of difference between
                                  these matching regions. This works well and
                                  is what most people want if they are working
                                  with long overlapping nucleic acid
                                  sequences. You are usually not interested in
                                  the non-overlapping ends of these
                                  sequences. If you have protein sequences or
                                  short RNA sequences however, you will be
                                  interested in differences at the very ends .
                                  It this option is set to be true then the
                                  differences at the ends will also be
                                  reported.

   Advanced (Unprompted) qualifiers: (none)
   Associated qualifiers:

   "-asequence" associated qualifiers
   -sbegin1            integer    Start of the sequence to be used
   -send1              integer    End of the sequence to be used
   -sreverse1          boolean    Reverse (if DNA)
   -sask1              boolean    Ask for begin/end/reverse
   -snucleotide1       boolean    Sequence is nucleotide
   -sprotein1          boolean    Sequence is protein
   -slower1            boolean    Make lower case
   -supper1            boolean    Make upper case
   -sformat1           string     Input sequence format
   -sdbname1           string     Database name
   -sid1               string     Entryname
   -ufo1               string     UFO features
   -fformat1           string     Features format
   -fopenfile1         string     Features file name

   "-bsequence" associated qualifiers
   -sbegin2            integer    Start of the sequence to be used
   -send2              integer    End of the sequence to be used
   -sreverse2          boolean    Reverse (if DNA)
   -sask2              boolean    Ask for begin/end/reverse
   -snucleotide2       boolean    Sequence is nucleotide
   -sprotein2          boolean    Sequence is protein
   -slower2            boolean    Make lower case
   -supper2            boolean    Make upper case
   -sformat2           string     Input sequence format
   -sdbname2           string     Database name
   -sid2               string     Entryname
   -ufo2               string     UFO features
   -fformat2           string     Features format
   -fopenfile2         string     Features file name

   "-outfile" associated qualifiers
   -rformat3           string     Report format
   -rname3             string     Base file name
   -rextension3        string     File name extension
   -rdirectory3        string     Output directory
   -raccshow3          boolean    Show accession number in the report
   -rdesshow3          boolean    Show description in the report
   -rscoreshow3        boolean    Show the score in the report
   -rstrandshow3       boolean    Show the nucleotide strand in the report
   -rusashow3          boolean    Show the full USA in the report
   -rmaxall3           integer    Maximum total hits to report
   -rmaxseq3           integer    Maximum hits to report for one sequence

   "-aoutfeat" associated qualifiers
   -offormat4          string     Output feature format
   -ofopenfile4        string     Features file name
   -ofextension4       string     File name extension
   -ofdirectory4       string     Output directory
   -ofname4            string     Base file name
   -ofsingle4          boolean    Separate file for each entry

   "-boutfeat" associated qualifiers
   -offormat5          string     Output feature format
   -ofopenfile5        string     Features file name
   -ofextension5       string     File name extension
   -ofdirectory5       string     Output directory
   -ofname5            string     Base file name
   -ofsingle5          boolean    Separate file for each entry

   General qualifiers:
   -auto               boolean    Turn off prompts
   -stdout             boolean    Write first file to standard output
   -filter             boolean    Read first file from standard input, write
                                  first file to standard output
   -options            boolean    Prompt for standard and additional values
   -debug              boolean    Write debug output to program.dbg
   -verbose            boolean    Report some/full command line options
   -help               boolean    Report command line options and exit. More
                                  information on associated and general
                                  qualifiers can be found with -help -verbose
   -warning            boolean    Report warnings
   -error              boolean    Report errors
   -fatal              boolean    Report fatal errors
   -die                boolean    Report dying program messages
   -version            boolean    Report version number and exit

ID   X65923; SV 1; linear; mRNA; STD; HUM; 518 BP.
XX
AC   X65923;
XX
DT   13-MAY-1992 (Rel. 31, Created)
DT   18-APR-2005 (Rel. 83, Last updated, Version 11)
XX
DE   H.sapiens fau mRNA
XX
KW   fau gene.
XX
OS   Homo sapiens (human)
OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
OC   Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae;
OC   Homo.
XX
RN   [1]
RP   1-518
RA   Michiels L.M.R.;
RT   ;
RL   Submitted (29-APR-1992) to the EMBL/GenBank/DDBJ databases.
RL   L.M.R. Michiels, University of Antwerp, Dept of Biochemistry,
RL   Universiteisplein 1, 2610 Wilrijk, BELGIUM
XX
RN   [2]
RP   1-518
RX   PUBMED; 8395683.
RA   Michiels L., Van der Rauwelaert E., Van Hasselt F., Kas K., Merregaert J.;
RT   "fau cDNA encodes a ubiquitin-like-S30 fusion protein and is expressed as
RT   an antisense sequence in the Finkel-Biskis-Reilly murine sarcoma virus";
RL   Oncogene 8(9):2537-2546(1993).
XX
DR   H-InvDB; HIT000322806.
XX
FH   Key             Location/Qualifiers
FH
FT   source          1..518
FT                   /organism="Homo sapiens"
FT                   /chromosome="11q"
FT                   /map="13"
FT                   /mol_type="mRNA"
FT                   /clone_lib="cDNA"
FT                   /clone="pUIA 631"
FT                   /tissue_type="placenta"
FT                   /db_xref="taxon:9606"
FT   misc_feature    57..278
FT                   /note="ubiquitin like part"
FT   CDS             57..458
FT                   /gene="fau"
FT                   /db_xref="GDB:135476"
FT                   /db_xref="GOA:P35544"
FT                   /db_xref="GOA:P62861"
FT                   /db_xref="HGNC:3597"
FT                   /db_xref="InterPro:IPR000626"
FT                   /db_xref="InterPro:IPR006846"
FT                   /db_xref="InterPro:IPR019954"
FT                   /db_xref="InterPro:IPR019955"
FT                   /db_xref="InterPro:IPR019956"
FT                   /db_xref="UniProtKB/Swiss-Prot:P35544"
FT                   /db_xref="UniProtKB/Swiss-Prot:P62861"
FT                   /protein_id="CAA46716.1"
FT                   /translation="MQLFVRAQELHTFEVTGQETVAQIKAHVASLEGIAPEDQVVLLAG
FT                   APLEDEATLGQCGVEALTTLEVAGRMLGGKVHGSLARAGKVRGQTPKVAKQEKKKKKTG
FT                   RAKRRMQYNRRFVNVVPTFGKKKGPNANS"
FT   misc_feature    98..102
FT                   /note="nucleolar localization signal"
FT   misc_feature    279..458
FT                   /note="S30 part"
FT   polyA_signal    484..489
FT   polyA_site      509
XX
SQ   Sequence 518 BP; 125 A; 139 C; 148 G; 106 T; 0 other;
     ttcctctttc tcgactccat cttcgcggta gctgggaccg ccgttcagtc gccaatatgc        60
     agctctttgt ccgcgcccag gagctacaca ccttcgaggt gaccggccag gaaacggtcg       120
     cccagatcaa ggctcatgta gcctcactgg agggcattgc cccggaagat caagtcgtgc       180
     tcctggcagg cgcgcccctg gaggatgagg ccactctggg ccagtgcggg gtggaggccc       240
     tgactaccct ggaagtagca ggccgcatgc ttggaggtaa agttcatggt tccctggccc       300
     gtgctggaaa agtgagaggt cagactccta aggtggccaa acaggagaag aagaagaaga       360
     agacaggtcg ggctaagcgg cggatgcagt acaaccggcg ctttgtcaac gttgtgccca       420
     cctttggcaa gaagaagggc cccaatgcca actcttaagt cttttgtaat tctggctttc       480
     tctaataaaa aagccactta gttcagtcaa aaaaaaaa                               518
//

ID   AY411291; SV 1; linear; genomic DNA; GSS; HUM; 402 BP.
XX
AC   AY411291;
XX
DT   13-DEC-2003 (Rel. 78, Created)
DT   17-DEC-2003 (Rel. 78, Last updated, Version 2)
XX
DE   Homo sapiens FAU gene, VIRTUAL TRANSCRIPT, partial sequence, genomic survey
DE   sequence.
XX
KW   GSS.
XX
OS   Homo sapiens (human)
OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
OC   Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae;
OC   Homo.
XX
RN   [1]
RP   1-402
RX   DOI; 10.1126/science.1088821.
RX   PUBMED; 14671302.
RA   Clark A.G., Glanowski S., Nielson R., Thomas P., Kejariwal A., Todd M.A.,
RA   Tanenbaum D.M., Civello D.R., Lu F., Murphy B., Ferriera S., Wang G.,
RA   Zheng X.H., White T.J., Sninsky J.J., Adams M.D., Cargill M.;
RT   "Inferring nonneutral evolution from human-chimp-mouse orthologous gene
RT   trios";
RL   Science 302(5652):1960-1963(2003).
XX
RN   [2]
RP   1-402
RA   Clark A.G., Glanowski S., Nielson R., Thomas P., Kejariwal A., Todd M.A.,
RA   Tanenbaum D.M., Civello D.R., Lu F., Murphy B., Ferriera S., Wang G.,
RA   Zheng X.H., White T.J., Sninsky J.J., Adams M.D., Cargill M.;
RT   ;
RL   Submitted (16-NOV-2003) to the EMBL/GenBank/DDBJ databases.
RL   Celera Genomics, 45 West Gude Drive, Rockville, MD 20850, USA
XX
CC   This sequence was made by sequencing genomic exons and ordering
CC   them based on alignment.
XX
FH   Key             Location/Qualifiers
FH
FT   source          1..402
FT                   /organism="Homo sapiens"
FT                   /mol_type="genomic DNA"
FT                   /db_xref="taxon:9606"
FT   gene            <1..>402
FT                   /gene="FAU"
FT                   /locus_tag="HCM4175"
XX
SQ   Sequence 402 BP; 95 A; 110 C; 129 G; 68 T; 0 other;
     atgcagctct ttgtccgcgc ccaggagcta cacaccttcg aggtgaccgg ccaggaaacg        60
     gtcgcccaga tcaaggctca tgtagcctca ctggagggca ttgccccgga agatcaagtc       120
     gtgctcctgg caggcgcgcc cctggaggat gaggccactc tgggccagtg cggggtggag       180
     gccctgacta ccctggaagt agcaggccgc atgcttggag gtaaagtcca tggttccctg       240
     gcccgtgctg gaaaagtgag aggtcagact cctaaggtgg ccaaacagga gaagaagaag       300
     aagaagacag gtcgggctaa gcggcggatg cagtacaacc ggcgctttgt caacgttgtg       360
     cccacctttg gcaagaagaa gggccccaat gccaactctt aa                          402
//

########################################
# Program: diffseq
# Rundate: Fri 15 Jul 2011 12:00:00
# Commandline: diffseq
#    [-asequence] tembl:x65923
#    [-bsequence] tembl:ay411291
# Report_format: diffseq
# Report_file: x65923.diffseq
# Additional_files: 2
# 1: X65923.diffgff (Feature file for first sequence)
# 2: AY411291.diffgff (Feature file for second sequence)
########################################

#=======================================
#
# Sequence: X65923     from: 1   to: 518
# HitCount: 1
#
# Compare: AY411291     from: 1   to: 402
# 
# X65923 overlap starts at 57
# AY411291 overlap starts at 1
# 
#
#=======================================


X65923 284-284 Length: 1
Feature: CDS 57-458 gene='fau' db_xref='GDB:135476' db_xref='GOA:P35544' db_xref='GOA:P62861' db_xref='HGNC:3597' db_xref='InterPro:IPR000626' db_xref='InterPro:IPR006846' db_xref='InterPro:IPR019954' db_xref='InterPro:IPR019955' db_xref='InterPro:IPR019956' db_xref='UniProtKB/Swiss-Prot:P35544' db_xref='UniProtKB/Swiss-Prot:P62861' protein_id='CAA46716.1'
Feature: misc_feature 279-458 note='S30 part'
Sequence: t
Sequence: c
Feature: gene 1-402 gene='FAU' locus_tag='HCM4175'
AY411291 228-228 Length: 1

#---------------------------------------
#
# Overlap_end: 458 in X65923
# Overlap_end: 402 in AY411291
# 
# SNP_count: 1
# Transitions: 1
# Transversions: 0
#
#---------------------------------------

#---------------------------------------
# Total_sequences: 2
# Total_length: 920
# Reported_sequences: 1
# Reported_hitcount: 1
#---------------------------------------

##gff-version 3
##sequence-region AY411291 1 402
#!Date 2011-07-15
#!Type DNA
#!Source-version EMBOSS 6.4.0.0
AY411291	diffseq	sequence_conflict	228	228	1.000	+	.	ID=AY411291.1;note=SNP in X65923;replace=t

##gff-version 3
##sequence-region X65923 1 518
#!Date 2011-07-15
#!Type DNA
#!Source-version EMBOSS 6.4.0.0
X65923	diffseq	sequence_conflict	284	284	1.000	+	.	ID=X65923.1;note=SNP in AY411291;replace=c