I have a DNA sequence of a protein and around 1200 zinc finger target sequences. These zinc finger target sequences are 9 bp long, resulting in BLASTn not finding them in the sequence. Needleman-Wunsch does find them, however, I can only search/align the DNA protein sequence with 1 zinc finger at a time. Is there a way to do this simultaneous (serial or parallel, computational time is not a big problem) for all 1200 zinc fingers and have the result in a table as with BLAST?
(I assume that by "DNA protein" you mean "coding DNA".)
"I can only search/align the sequence with 1 zinc finger at a time" - does this mean that you have not found out a way to do so, or that you desire to proceed in this fashion? I think that it is the first, based on the title of your question, but it is not at all clear what you are looking to do.
If you want to locate specific 9bp motifs in your sequence, then I can suggest this small piece of code that I wrote that looks for exact matches of specific sequences, that outputs a BLAST-like table. It is slow relative to BLASTN but it does not use the short-match-ignoring heuristics that BLASTN relies upon so it may be helpful.
The code was written in response to this bioinformatics SE question, which seems somewhat similar to your question here.
Note that you will have to input each expected 9bp query against the reference sequence in the form of a FASTA file.