Align EST and genomic DNA sequences emboss est2genome -estsequence $input1 -genomesequence $input2 -outfile $out_file1 -match $match -mismatch $mismatch -gappenalty $gappenalty -intronpenalty $intronpenalty -splicepenalty $splicepenalty -minscore $minscore -reverse $reverse -splice $splice -mode $mode -best $best -shuffle $shuffle -seed $seed -align $align -width $width -auto EST sequence(s) Genomic sequence Score for matching two bases Cost for mismatching two bases Cost for deleting a single base in either sequence, excluding introns Cost for an intron, independent of length Cost for an intron, independent of length and starting/ending on donor-acceptor sites Exclude alignments with scores below this threshold score Reverse the orientation of the EST sequence No Yes Use donor and acceptor splice sites Yes No Comparison mode Both strands Forward strand only Reverse strand only Only best comparisons Yes No Shuffle Random number seed Show the alignment No Yes Alignment width

.. class:: warningmark The input dataset needs to be sequences. ----- You can view the original documentation here_. .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/est2genome.html