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       gmap - Genomic Mapping and Alignment Program


       gmap -dDB|-gFASTA [OPTION]... [QUERY]...


       Align  the  sequences  QUERY to the reference, specified with -d or -g.
       With no QUERY, read standard input.


   Input options
       -D, --dir=directory
              Genome directory

       -d, --db=STRING
              Genome database.  If argument is ’?’  (with  the  quotes),  this
              command lists available databases.

       -G, --genomefull
              Use  full  genome  (all  ASCII  chars  allowed; built explicitly
              during setup), not compressed version

       -g, --gseg=filename
              User-suppled genomic segment

       -q, --jobdiv=INT/INT
              Process only i out of every n sequences e.g., 0/100 or 99/100

   Computation options
       -B, --batch=INT
              Batch mode (0 = no pre-loading, 1 =  pre-load  only  indices;  2
              (default) = pre-load both indices and genome)

       -K, --intronlength=INT
              Max length for one intron (default 1000000)

       -L, --totallength=INT
              Max total intron length (default 2400000)

       -x, --chimera_margin=INT
              Amount  of unaligned sequence that triggers search for a chimera
              (default off)

       -w, --reference=filename
              Reference cDNA sequence for relative alignment

       -t, --nthreads=INT
              Number of worker threads

       -s, --altstrain
              Search alternate strains in addition

       -C, --chrsubsetfile=filename
              User-suppled chromosome subset file

       -c, --chrsubset=string
              Chromosome subset to search

       -z, --direction=STRING
              cDNA direction (sense, antisense, or auto (default))

       -H, --trimendexons=INT
              Trim end exons with fewer than given number of matches  (in  nt,
              default 12)

       -X, --canonical=INT
              Reward  for  canonical  and semi-canonical introns 0=low reward,
              1=high  reward  (default),  2=low   reward   for   high-identity
              sequences and high reward otherwise

       -p, --prunelevel
              Pruning level: 0=no pruning (default), 1=poor seqs, 2=repetitive
              seqs, 3=poor and repetitive

   Output types
       -S, --summary
              Show summary of alignments only

       -A, --align
              Show alignments

       -3, --continuous
              Show alignment in three continuous lines

       -4, --alignedexons
              Show alignment in three lines per exon

       -Z, --compress
              Print output in compressed format

       -E, --exons=STRING
              Print exons ("cdna" or "genomic")

       -P, --protein_dna
              Print protein sequence (cDNA)

       -Q, --protein_gen
              Print protein sequence (genomic)

       -f, --format=INT
              Format for output
               1 = PSL (BLAT) format,
               2 = GFF3 gene format,
               3 = GFF3 match format,
               6 = splicesites output (for GSNAP),
               7 = IIT FASTA exon map format,
               8 = IIT FASTA map format,
               9 = coords in table format

   Output options
       -n, --npaths=INT
              Maximum number of paths to show.  If set to 0, prints two  paths
              if chimera detected, else one.

       -O, --ordered
              Print  output  in same order as input (relevant only if there is
              more than one worker thread)

       -5, --md5
              Print MD5 checksum for each query sequence

       -o, --chimera_overlap
              Overlap to show, if any, at chimera breakpoint

       -V, --usesnps=STRING
              Use database  containing  known  SNPs  (in  <STRING>.iit,  built
              previously using snpindex) for reporting output

       -F, --fulllength
              Assume full-length protein, starting with Met

       -T, --truncate
              Truncate  alignment  around  full-length  protein,  Met  to Stop
              Implies -F flag.

       -Y, --tolerant
              Translates cDNA with corrections for frameshifts

   External map file options
       -M, --mapdir=directory
              Map directory

       -m, --map=iitfile
              Map file.  If argument is ’?’  (with  the  quotes),  this  lists
              available map files.

       -e, --mapexons
              Map each exon separately

       -b, --mapboth
              Report hits from both strands of genome

       -u, --flanking=INT
              Show flanking hits (default 0)

   Alignment output options
       -N, --nolengths
              No intron lengths in alignment

       -I, --invertmode=INT
              Mode for alignments to genomic (-) strand:
               0=Don’t invert the cDNA (default)
               1=Invert cDNA and print genomic (-) strand
               2=Invert cDNA and print genomic (+) strand

       -i, --introngap=INT
              Nucleotides to show on each end of intron (default=3)

       -l, --wraplength=INT
              Wrap length for alignment (default=50)

   Help options
       -v, --version
              Show version

       -?, --help
              Show this help message


       GMAPDB genome directory (eqivalent to -D)


              configuration file


       Thomas D. Wu and Colin K. Watanabe


       Report bugs to Thomas Wu <>.


       Copyright 2005 Genentech, Inc. All rights reserved.


       gmap_setup(1), gsnap(1)