With this option you can:
01.. Trim an exactly defined number of basepairs from the
the 5' - end, or from the 3' - end or from both ends.
02.. Remove poly-A tails from the 3' - end
03.. Specifiy the quality files which should be trimmed
by exactly in the same way as the ESTs. When you want to use quality sequences for your SNP identification the qualtiy sequences have to be in the same 'frame' as the ESTs and have to have the same length as the ESTs. This may be achieved with this option of PanGEA.
Choose trim sequences - remove poly-A tail. Press the 'Proceed' button.
Choose the regions which should be removed from the 3' end, or from the 5' end or from both ends. Check the 'poly-a box' box if you want to remove the poly-A tail instead. The algorithm searching for poly-A tails, only removes them from the 3'-ends. Only the first n-nucleotides (n has to be sepcified by the user) will be searched, beginning from the 3' end. If an initial succession of m-times 'A' is found (m has to be specified by the user), the algorithm assumes an poly-A tail at this position and searches for more 'A' nucleotides, now even tolerating a limited amount of mismatches. Everything which is 3' to the start position of the poly-A tail will be removed. If quality sequences have been specified the same equivalent of nucleotides will be removed from the quality sequences.
Choose the input files. Files have to be multiple fast-files. You may even specifiy the quality files, they will be trimmed in the same way as the fasta-files.
Press the 'Proceed' button.
Read the report and press the 'New task' button.