I'm having trouble aligning 3 sequences together - the total gene (~2500bp) and the forward and reverse sequences that are ~1000bp in length. Now I'm using Clustal X2, but the problem is that the program does complete alignment, which is useless for me right now. Could anyone recommend or suggest any parameters or methods on how to align more that 2 sequences together, but that each sequence is aligned to the first one (the total gene)? Thanks!
Your question is not very clear, but I think what you are trying to do is align sequencing results to a reference gene sequence.
Your total gene sequence spans ~2500 bp. It sounds like you have a forward sequence at the start of gene, reading only about 1000 bp and the reverse strand reading in 1000 bp from the end (if this is Sanger sequencing, you likely only have 800-900 bp of accurate base reads by the way). Therefore, you have a gap of about 500 bp in the middle of your gene of interest.
There are (at least) two ways to do the alignment, and I would suggest the manual method if you are trying to verify gene sequencing.
At the top of this window is a schematic, showing exactly how much of the the query sequence aligns with the subject sequence. The longer the line, the more bases align. Similarly, the closer the colour of the line is to right of the scale (e.g., red), then the more continuous the segment is indicating a longer, continuous alignment.
Below the graphic is a table of results. Briefly, the table highlights all possible alignments that the BLAST algorithm has found, including how much coverage there was, confidence of the alignment and length of alignment coverage.
Below the results table, are the detailed results which were summarized in the table. This detailed report shows you exactly which bases align or mismatch, or any gaps. The top line is the subject sequence; the bottom is the query sequence. The other thing to keep in mind here is the Strand line. In this case, it says "Plus/Plus, meaning that the aligned sequences were the forward sense, or plus strand, of each of subject and query sequence, respectively. If you entered a reverse complement sequence instead (such as the reverse sequencing results) then this would change to "Plus/Minus".
From here, you will still need to manually line these results up to your gene of interest to determine exactly which portion of the gene is missing sequence coverage, as well as any mutations that may have cropped up in the cloning process.