Align EST and genomic DNA sequences Both strands Both strands Forward strand only Forward strand only Reverse strand only Reverse strand only qualifiers for parameter: estsequence qualifiers for parameter: genomesequence Score for matching two bases Score for matching two bases Cost for mismatching two bases Cost for mismatching two bases Gap penalty Cost for deleting a single base in either sequence, excluding introns Intron penalty Cost for an intron, independent of length. Splice site penalty Cost for an intron, independent of length and starting/ending on donor-acceptor sites Minimum accepted score Exclude alignments with scores below this threshold score. Reverse orientation Reverse the orientation of the EST sequence Use donor and acceptor splice sites Use donor and acceptor splice sites. If you want to ignore donor-acceptor sites then set this to be false. Comparison mode This determines the comparion mode. The default value is 'both', in which case both strands of the est are compared assuming a forward gene direction (ie GT/AG splice sites), and the best comparsion redone assuming a reversed (CT/AC) gene splicing direction. The other allowed modes are 'forward', when just the forward strand is searched, and 'reverse', ditto for the reverse strand. Print out only best alignment You can print out all comparisons instead of just the best one by setting this to be false. Space threshold (in megabytes) For linear-space recursion. If product of sequence lengths divided by 4 exceeds this then a divide-and-conquer strategy is used to control the memory requirements. In this way very long sequences can be aligned. If you have a machine with plenty of memory you can raise this parameter (but do not exceed the machine's physical RAM) Shuffle Shuffle Random number seed Random number seed Show the alignment Show the alignment. The alignment includes the first and last 5 bases of each intron, together with the intron width. The direction of splicing is indicated by angle brackets (forward or reverse) or ???? (unknown). Alignment width Alignment width Start the web service and receive the result. Blocks until job is finished. Start the web service and receive a job-id. Returns immediately. Wait until a job (by job-id) has finished. Blocks until job is finished. Get status information about a running job. Returns immediately. Get the results of a job (by job-id) Start the web service and receive the result. Blocks until job is finished. Start the web service and receive a job-id. Returns immediately. Wait until a job (by job-id) has finished. Blocks until job is finished. Get status information about a running job. Returns immediately. Get the results of a job (by job-id)