I am using the Biostrings package in R to translate my NGS reads directly to amino acids. It has been great so far in my analysis, but I need to modify it for a part of the analysis.

I am using a conserved genomic site to begin translating reads in the forward direction from the 5' end. However, if the read is truncated at the 5' end, I now need to start translating from the conserved site at the 3' end end to stay in frame. I believe I need to start reading the string at the -3 position and read each codon forward every -3 from that position? *It is fine if the output is 3' - 5'- I can use the reverse function to reverse the order of the amino acids. 

For example: 

5'  CTTGAGATGCGAATT  3'  

5'  - - - - AGATGCGAATT 3' 

The first one will translate in frame. The second read will not translate in frame. Thanks for any help/advice! 

Here is the code that I believe will need to be updated:

                         "last %d bases were ignored", phase);

                return 1;

        }

        return 0;

}

/*

 * --- .Call ENTRY POINT ---

 * Return an AAStringSet object.

 */

SEXP DNAStringSet_translate(SEXP x, SEXP base_codes, SEXP lkup, SEXP skipcode)

{

        cachedXStringSet X, Y;

        cachedCharSeq X_elt, Y_elt;

        char skipcode0;

        int ans_length, i, errcode;

        SEXP ans, width, ans_width;

        TwobitEncodingBuffer teb;

        X = _cache_XStringSet(x);

        skipcode0 = (unsigned char) INTEGER(skipcode)[0];

        ans_length = _get_cachedXStringSet_length(&X);

        PROTECT(width = NEW_INTEGER(ans_length));

        for (i = 0; i < ans_length; i++) {

                X_elt = _get_cachedXStringSet_elt(&X, i);

                INTEGER(width)[i] = X_elt.length / 3;

        }

        PROTECT(ans = alloc_XRawList("AAStringSet", "AAString", width));

        Y = _cache_XStringSet(ans);

        teb = _new_TwobitEncodingBuffer(base_codes, 3, 0);

        ans_width = _get_XStringSet_width(ans);

        for (i = 0; i < ans_length; i++) {

                X_elt = _get_cachedXStringSet_elt(&X, i);

                Y_elt = _get_cachedXStringSet_elt(&Y, i);

                errcode = translate(&X_elt, &Y_elt, &teb, lkup, skipcode0);

                if (errcode == -1) {

                        UNPROTECT(2);

                        if (ans_length == 1)

                                error("%s", errmsg_buf);

                        else

                                error("in 'x[[%d]]': %s", i + 1, errmsg_buf);

                }

                if (errcode == 1) {

                        if (ans_length == 1)

                                warning("%s", errmsg_buf);

                        else

                                warning("in 'x[[%d]]': %s", i + 1, errmsg_buf);

                }

                INTEGER(ans_width)[i] = Y_elt.length;

        }

        UNPROTECT(2);

        return ans;

}

Hi,

There is no need to start translating from the conserved site at the 3' end to stay in frame. When a read is truncated at the 5' end, all you need to do is trim 1 or 2 nucleotides on its 5' end to be in frame again. Or maybe you don't need to trim anything if the truncation preserved the frame. More precisely, assuming that the 3' of your read is in frame (i.e. its last 3 nucleotides form a codon), all you need to do is trim the 5' end by RL %% 3 where RL is the length of the read. If reads is the DNAStringSet containing your reads and Ltrim the integer vector parallel to reads containing the number of nucleotides you want to trim on the left end (i.e. 5' end) of each read, then trim the reads with windows(reads, start=1+Ltrim).

Hope this helps,

H.