Merge pull request #4 from dingquanyu/multimer-dataloader

created Multimer dataloader and datamodule classes

openfold/data/data_pipeline.py

@@ -803,7 +803,8 @@ class DataPipeline:
     def _parse_template_hits(
             self,
             alignment_dir: str,
-            alignment_index: Optional[Any] = None
+            alignment_index: Optional[Any] = None,
+            input_sequence=None,
     ) -> Mapping[str, Any]:
         all_hits = {}
         if (alignment_index is not None):
@@ -830,6 +831,15 @@ class DataPipeline:
                     with open(path, "r") as fp:
                         hits = parsers.parse_hhr(fp.read())
                     all_hits[f] = hits
+                    fp.close()
+                    
+                elif (ext =='.sto') and (f.startswith("pdb")):
+                    with open(path,"r") as fp:
+                        hits = parsers.parse_hmmsearch_sto(fp.read(),input_sequence)
+                    all_hits[f] = hits
+                    fp.close()
+        return all_hits
+
 
     def _get_msas(self,
         alignment_dir: str,
@@ -937,7 +947,7 @@ class DataPipeline:
         input_sequence = mmcif.chain_to_seqres[chain_id]
         hits = self._parse_template_hits(
             alignment_dir,
-            alignment_index)
+            alignment_index,input_sequence)
 
         template_features = make_template_features(
             input_sequence,
@@ -986,7 +996,7 @@ class DataPipeline:
 
         hits = self._parse_template_hits(
             alignment_dir,
-            alignment_index
+            alignment_index,input_sequence
         )
 
         template_features = make_template_features(
@@ -1018,7 +1028,7 @@ class DataPipeline:
 
         hits = self._parse_template_hits(
             alignment_dir,
-            alignment_index
+            alignment_index,input_sequence
         )
 
         template_features = make_template_features(
@@ -1107,7 +1117,7 @@ class DataPipeline:
             alignment_dir = os.path.join(
                 super_alignment_dir, desc
             )
-            hits = self._parse_template_hits(alignment_dir, alignment_index=None)
+            hits = self._parse_template_hits(alignment_dir, alignment_index=None,input_sequence=input_sequence)
             template_features = make_template_features(
                 seq,
                 hits,

openfold/data/feature_pipeline.py

@@ -134,8 +134,8 @@ class FeaturePipeline:
         mode: str = "train",
         is_multimer: bool = False,
     ) -> FeatureDict:
-        if(is_multimer and mode != "predict"):
-            raise ValueError("Multimer mode is not currently trainable")
+        # if(is_multimer and mode != "predict"):
+        #     raise ValueError("Multimer mode is not currently trainable")
         
         return np_example_to_features(
             np_example=raw_features,

openfold/data/input_pipeline.py

@@ -104,7 +104,7 @@ def ensembled_transform_fns(common_cfg, mode_cfg, ensemble_seed):
         # the masked locations and secret corrupted locations.
         transforms.append(
             data_transforms.make_masked_msa(
-                common_cfg.masked_msa, mode_cfg.masked_msa_replace_fraction
+                common_cfg.masked_msa, mode_cfg.masked_msa_replace_fraction,seed=msa_seed
             )
         )
 

openfold/utils/loss.py

@@ -1667,7 +1667,7 @@ def chain_center_of_mass_loss(
     all_atom_positions = all_atom_positions[..., ca_pos, :]
     all_atom_mask = all_atom_mask[..., ca_pos: (ca_pos + 1)]  # keep dim
     chains, _ = asym_id.unique(return_counts=True)
-    one_hot = torch.nn.functional.one_hot(asym_id.to(torch.int64), 
+    one_hot = torch.nn.functional.one_hot(asym_id.to(torch.int64)-1, # have to reduce asym_id by one because class values must be smaller than num_classes  
                                           num_classes=chains.shape[0]).to(dtype=all_atom_mask.dtype) # make sure asym_id dtype is int
     one_hot = one_hot * all_atom_mask
     chain_pos_mask = one_hot.transpose(-2, -1)
@@ -1749,7 +1749,7 @@ def get_optimal_transform(
             src_atoms = torch.zeros((1, 3), device=src_atoms.device).float()
             tgt_atoms = src_atoms
         else:
-            src_atoms = src_atoms[mask, :]
+            src_atoms = src_atoms.to('cuda:0')[mask, :]
             tgt_atoms = tgt_atoms.to('cuda:0')[mask, :]
     src_center = src_atoms.mean(-2, keepdim=True)
     tgt_center = tgt_atoms.mean(-2, keepdim=True)
@@ -1857,7 +1857,6 @@ def greedy_align(
         best_idx = None
         cur_asym_list = entity_2_asym_list[int(cur_entity_ids)]
         cur_residue_index = per_asym_residue_index[int(cur_asym_id)]
-        
         cur_pred_pos = pred_ca_pos[asym_mask]
         cur_pred_mask = pred_ca_mask[asym_mask]
         for next_asym_id in cur_asym_list:
@@ -1881,35 +1880,28 @@ def greedy_align(
     return align
 
 
-def merge_labels(batch, per_asym_residue_index, labels, align):
+def merge_labels(per_asym_residue_index, labels, align):
     """
-    batch:
-    labels: list of label dicts, each with shape [nk, *]
-    align: list of int, such as [2, None, 0, 1], each entry specify the corresponding label of the asym.
+    per_asym_residue_index: A dictionary that record which asym_id corresponds to which regions of residues in the multimer complex.
+    labels: list of original ground truth feats
+    align: list of tuples, each entry specify the corresponding label of the asym.
     """
-    num_res = batch["msa_mask"].shape[-1]
     outs = {}
     for k, v in labels[0].items():
-        if k in [
-            "resolution",
-        ]:
-            continue
         cur_out = {}
         for i, j in align:
             label = labels[j][k]
+            cur_num_res = labels[j]['aatype'].shape[-1]
             # to 1-based
             cur_residue_index = per_asym_residue_index[i + 1]
-            cur_out[i] = label[cur_residue_index]
+            if len(v.shape)==0 or "template" in k:
+                continue
+            else:    
+                dimension_to_merge = label.shape.index(cur_num_res) if cur_num_res in label.shape else 0
+                cur_out[i] = label.index_select(dimension_to_merge,cur_residue_index)
         cur_out = [x[1] for x in sorted(cur_out.items())]
-        new_v = torch.concat(cur_out, dim=0)
-        merged_nres = new_v.shape[0]
-        assert (
-            merged_nres <= num_res
-        ), f"bad merged num res: {merged_nres} > {num_res}. something is wrong."
-        if merged_nres < num_res:  # must pad
-            pad_dim = new_v.shape[1:]
-            pad_v = new_v.new_zeros((num_res - merged_nres, *pad_dim))
-            new_v = torch.concat((new_v, pad_v), dim=0)
+        if len(cur_out)>0:
+            new_v = torch.concat(cur_out, dim=dimension_to_merge)
             outs[k] = new_v
     return outs
 
@@ -2050,7 +2042,6 @@ class AlphaFoldMultimerLoss(AlphaFoldLoss):
         true_ca_masks = [
             l["all_atom_mask"][..., ca_idx].float() for l in labels
         ]  # list([nres,])
-
         unique_asym_ids = torch.unique(batch["asym_id"])
 
         per_asym_residue_index = {}
@@ -2059,7 +2050,6 @@ class AlphaFoldMultimerLoss(AlphaFoldLoss):
             per_asym_residue_index[int(cur_asym_id)] = batch["residue_index"][asym_mask]
 
         anchor_gt_asym, anchor_pred_asym = get_least_asym_entity_or_longest_length(batch)
-        print(f"anchor_gt_asym is : {anchor_gt_asym} and anchor_pred_asym is {anchor_pred_asym}")
         anchor_gt_idx = int(anchor_gt_asym) - 1
 
         unique_entity_ids = torch.unique(batch["entity_id"])
@@ -2100,16 +2090,13 @@ class AlphaFoldMultimerLoss(AlphaFoldLoss):
         del aligned_true_ca_poses
         del r,x
         gc.collect()
-
+        print(f"finished multi-chain permutation and final align is {align}")
         merged_labels = merge_labels(
-            batch,
             per_asym_residue_index,
             labels,
             align,
         )
                 
-        print(f"finished multi-chain permutation and final align is {align}")
-                
         return merged_labels
 
     def forward(self,out,batch,_return_breakdown=False):
@@ -2122,9 +2109,9 @@ class AlphaFoldMultimerLoss(AlphaFoldLoss):
         batch: a pair of input features and its corresponding ground truth structure
         """
         features,labels = batch
-        features['resolution'] = labels[2]['resolution'] # firstly update the resolution feature
         # first remove the recycling dimention of input features
         features = tensor_tree_map(lambda t: t[..., -1], features)
+        features['resolution'] = labels[0]['resolution']
         # then permutate ground truth chains before calculating the loss
         permutated_labels = self.multi_chain_perm_align(out,features,labels)
         permutated_labels.pop('aatype')

tests/test_data/alignments/1psm_A/bfd_uniclust_hits.a3m

+>query
+EAYKKAKQASQDAEQAAKDAENASKEAEEAAKEAVNLK
+>tr|A0A024VQI0|A0A024VQI0_PLAFA Uncharacterized protein OS=Plasmodium falciparum FCH/4 GN=PFFCH_02010 PE=4 SV=1
+EAYKKAKEASQDAEKAAEEAEKAAEQAEQASKDAEKLK
+>tr|A0A151L2U9|A0A151L2U9_PLARE Merozoite surface protein 3 (Fragment) OS=Plasmodium reichenowi GN=PRSY57_0014700A PE=4 SV=1
+-KAKKASEDAEKVKKASEDaekaakdAENASKEAEEAAQEAVKLK
+>tr|O15855|O15855_PLAFA Merozoite surface protein 3 (Fragment) OS=Plasmodium falciparum GN=SPAM PE=4 SV=1
+-KAKKASEDAEKAA-----ndAENASKEAEEAAKEAVNLK
+>tr|W7JBM4|W7JBM4_PLAFA Uncharacterized protein OS=Plasmodium falciparum UGT5.1 GN=C923_03131 PE=4 SV=1
+-KAKKASEDAGNASKEAE---EASCHKQNILY------
+>tr|A0A1D8H334|A0A1D8H334_PLAFA Merozoite surface protein-3 (Fragment) OS=Plasmodium falciparum OX=5833 PE=4 SV=1 
+------KKASEDAEKAANDAENASKEAEEASKEAVNLK
+>tr|A0A2P9DFY8|A0A2P9DFY8_PLARE Merozoite surface protein 3 OS=Plasmodium reichenowi OX=5854 GN=PRG01_1033900 PE=4 SV=1
+DAYKKAKEAAEGAEKAAEEAEKAAEQAEQASKDAEKLK
+>tr|A0A2P9GM08|A0A2P9GM08_9APIC Merozoite surface protein 3 OS=Plasmodium sp. DRC-Itaito OX=720590 GN=PBILCG01_1034200 PE=4 SV=1
+ETYKKVKQASQDAEQAAEKAEKAAKDAEQASKDAEKLK
+>tr|A0A2S1Q7P9|A0A2S1Q7P9_PLAFA Merozoite surface protein 3 (Fragment) OS=Plasmodium falciparum OX=5833 PE=4 SV=1
+EAYKKAKQASQDAEQAAKDAEQAAKDAEQASKDAEKLK
+>tr|A0A2P9C2Y3|A0A2P9C2Y3_9APIC Merozoite surface protein 3 OS=Plasmodium gaboni OX=647221 GN=PGABG01_1033300 PE=4 SV=1
+---IIVKKEAQKAKEAAQTAEkekdisEN---AKNSAVSAKSSK
+>tr|A0A060RU34|A0A060RU34_PLARE Merozoite surface protein 3 OS=Plasmodium reichenowi OX=5854 GN=MSP3 PE=4 SV=1
+---LKAKKASEDAEKA---AEdaeNASKEAEEAAQEAVKLK
+>tr|W4J2M7|W4J2M7_PLAFP Uncharacterized protein OS=Plasmodium falciparum (isolate Palo Alto / Uganda) OX=57270 GN=PFUGPA_01621 PE=4 SV=1
+---LKAKKASEDAGNAS-------KEAEEASWFRVQ--

tests/test_data/alignments/1psm_A/mgnify_hits.sto

+# STOCKHOLM 1.0
+
+#=GS MGYP000005532851/48-76   DE [subseq from] PL=00 UP=0 BIOMES=0110000000000
+#=GS MGYP000005532851/81-108  DE [subseq from] PL=00 UP=0 BIOMES=0110000000000
+#=GS MGYP000005532851/110-139 DE [subseq from] PL=00 UP=0 BIOMES=0110000000000
+#=GS MGYP000091056102/48-76   DE [subseq from] PL=01 UP=0 BIOMES=0110000000000
+#=GS MGYP000091056102/81-108  DE [subseq from] PL=01 UP=0 BIOMES=0110000000000
+#=GS MGYP000091056102/110-139 DE [subseq from] PL=01 UP=0 BIOMES=0110000000000
+#=GS MGYP000091056102/174-199 DE [subseq from] PL=01 UP=0 BIOMES=0110000000000
+#=GS MGYP000091056102/252-279 DE [subseq from] PL=01 UP=0 BIOMES=0110000000000
+
+query                            EAYKKAKQASQDAEQAAKDAENASKEAEEAAKEAVNLK
+MGYP000005532851/48-76           -----AKQASLDAKQASVDAKHESVVAKQASLEA----
+MGYP000005532851/81-108          ---VVAKQASVDAKQASVDAKHESVVAKQAS-------
+MGYP000005532851/110-139         ----VAKQASLDAKQASLDAKQASLDAKQASVDA----
+MGYP000091056102/48-76           -----AKQASLDAKQASVDAKHESVVAKQASLEA----
+MGYP000091056102/81-108          ---VVAKQASVDAKQASVDAKHESVVAKQAS-------
+MGYP000091056102/110-139         ----VAKQASLDAKQASLDAKQASLDAKQASVDA----
+MGYP000091056102/174-199         -----AKQASLDAKQASVDAKHESVVAKQAS-------
+MGYP000091056102/252-279         ------KQASVDAKQASVDAKQASVDAKQASVDA----
+#=GC RF                          xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
+//

tests/test_data/alignments/1psm_A/uniref90_hits.sto

+# STOCKHOLM 1.0
+
+#=GS UniRef90_Q9NIG6/58-95          DE [subseq from] Merozoite surface protein 3 (Fragment) n=1 Tax=Plasmodium falciparum TaxID=5833 RepID=Q9NIG6_PLAFA
+#=GS UniRef90_A0A024VYN0/90-127     DE [subseq from] Merozoite surface protein 3 n=52 Tax=Plasmodium falciparum TaxID=5833 RepID=A0A024VYN0_PLAFA
+#=GS UniRef90_UPI0019011389/487-495 DE [subseq from] potassium voltage-gated channel subfamily C member 1-like n=1 Tax=Salvelinus namaycush TaxID=8040 RepID=UPI0019011389
+#=GS UniRef90_O15863/57-94          DE [subseq from] Merozoite surface protein 3 (Fragment) n=10 Tax=Plasmodium falciparum TaxID=5833 RepID=O15863_PLAFA
+#=GS UniRef90_A0A6J8EZW5/149-173    DE [subseq from] Secreted protein n=1 Tax=Mytilus coruscus TaxID=42192 RepID=A0A6J8EZW5_MYTCO
+#=GS UniRef90_A0A8C3V826/99-123     DE [subseq from] Translation initiation factor IF-2 n=1 Tax=Catharus ustulatus TaxID=91951 RepID=A0A8C3V826_CATUS
+#=GS UniRef90_A0A8C3V826/170-202    DE [subseq from] Translation initiation factor IF-2 n=1 Tax=Catharus ustulatus TaxID=91951 RepID=A0A8C3V826_CATUS
+#=GS UniRef90_O15854/44-77          DE [subseq from] Merozoite surface protein 3 (Fragment) n=2 Tax=Plasmodium falciparum TaxID=5833 RepID=O15854_PLAFA
+#=GS UniRef90_A0A401U021/46-73      DE [subseq from] CG2 omega repeat (Fragment) n=1 Tax=Chiloscyllium punctatum TaxID=137246 RepID=A0A401U021_CHIPU
+#=GS UniRef90_UPI001F20CBA7/9-40    DE [subseq from] hypothetical protein n=1 Tax=Niallia circulans TaxID=1397 RepID=UPI001F20CBA7
+#=GS UniRef90_UPI001F20CBA7/36-61   DE [subseq from] hypothetical protein n=1 Tax=Niallia circulans TaxID=1397 RepID=UPI001F20CBA7
+#=GS UniRef90_UPI001F20CBA7/64-88   DE [subseq from] hypothetical protein n=1 Tax=Niallia circulans TaxID=1397 RepID=UPI001F20CBA7
+#=GS UniRef90_A0A1D8H334/1-33       DE [subseq from] Merozoite surface protein-3 (Fragment) n=1 Tax=Plasmodium falciparum TaxID=5833 RepID=A0A1D8H334_PLAFA
+#=GS UniRef90_A0A3M0JR79/4-33       DE [subseq from] Protein Wnt n=22 Tax=Neognathae TaxID=8825 RepID=A0A3M0JR79_HIRRU
+#=GS UniRef90_A0A3M0JR79/40-67      DE [subseq from] Protein Wnt n=22 Tax=Neognathae TaxID=8825 RepID=A0A3M0JR79_HIRRU
+#=GS UniRef90_A0A3M0JR79/67-98      DE [subseq from] Protein Wnt n=22 Tax=Neognathae TaxID=8825 RepID=A0A3M0JR79_HIRRU
+#=GS UniRef90_A0A3M0JR79/95-124     DE [subseq from] Protein Wnt n=22 Tax=Neognathae TaxID=8825 RepID=A0A3M0JR79_HIRRU
+#=GS UniRef90_A0A159SN41/45-78      DE [subseq from] Merozoite surface protein 3 (Fragment) n=2 Tax=Plasmodium falciparum TaxID=5833 RepID=A0A159SN41_PLAFA
+#=GS UniRef90_A0A159SLY0/58-95      DE [subseq from] Merozoite surface protein 3 (Fragment) n=2 Tax=Plasmodium falciparum TaxID=5833 RepID=A0A159SLY0_PLAFA
+
+query                                  EAYKKAKQASQDAEQAAKDAENASKEAEEAAKEAVNLK
+UniRef90_Q9NIG6/58-95                  EAYKKAKQASQDAEQAAKDAENASKEAEEAAKEAVNLK
+UniRef90_A0A024VYN0/90-127             EAYKKAKQASQDAEQAAKDAENASKEAEEAAKEAVNLK
+UniRef90_UPI0019011389/487-495         ------------------------KDARQVIKD-----
+UniRef90_O15863/57-94                  EAYKKAKQASQDAEQAAKDAEQAAKDAEQASKDAEKLK
+UniRef90_A0A6J8EZW5/149-173            -------QACKDLGQACKDLEQACKDIGQACK------
+UniRef90_A0A8C3V826/99-123             -AVRDAPNAVRDAPNAVRDAPNAVRD------------
+UniRef90_A0A8C3V826/170-202            --VRDAPKAVRDAPNAVRDAPNAVRDAPNAVRDAP---
+UniRef90_O15854/44-77                  ----KAKKASEDAEKAANDAENASKEAEEAAKEAVNLK
+UniRef90_A0A401U021/46-73              --------GNKDSDNGTKDSDNGTKDSDNGTKESDN--
+UniRef90_UPI001F20CBA7/9-40            --RKDVEMARKDVEVARKDVEVARKDVEVASKDA----
+UniRef90_UPI001F20CBA7/36-61           --------ASKDAEVASKDAEVASKDAEVASKDV----
+UniRef90_UPI001F20CBA7/64-88           --------ASKDVEVASKDVEVASKDVEVARKD-----
+UniRef90_A0A1D8H334/1-33               -----AKKASEDAEKAANDAENASKEAEEASKEAVNLK
+UniRef90_A0A3M0JR79/4-33               ---RSAEQISEDAEQISEDAEQISKVAEQISEV-----
+UniRef90_A0A3M0JR79/40-67              ----DAEQISEDAEQISEDAEQISKVAEQISK------
+UniRef90_A0A3M0JR79/67-98              ---KVAEQISEDAEQISEDAEQISKDAEQISKDAE---
+UniRef90_A0A3M0JR79/95-124             ---KDAEQISEDAGQISEDAEQISEDAEQISSL-----
+UniRef90_A0A159SN41/45-78              ----KAKKASEDAEKAANDAENASKEAEEAAKEAVNLK
+UniRef90_A0A159SLY0/58-95              EAYKKAKQASQDAEQAAKDAEQAAKDAEQASKDAEKLK
+#=GC RF                                xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
+//

tests/test_data/alignments/2crb_A/mgnify_hits.sto

+# STOCKHOLM 1.0
+
+#=GS MGYP000613015979/52-138  DE [subseq from] PL=11 UP=0 BIOMES=0000000011000
+#=GS MGYP000356782790/15-100  DE [subseq from] PL=01 UP=0 BIOMES=1000000000000
+#=GS MGYP000745946800/67-150  DE [subseq from] PL=00 UP=0 BIOMES=0000000011000
+#=GS MGYP000365627167/34-120  DE [subseq from] PL=01 UP=0 BIOMES=1000000000000
+#=GS MGYP000326981611/4-88    DE [subseq from] PL=00 UP=0 BIOMES=0000000011000
+#=GS MGYP000438079158/44-95   DE [subseq from] PL=10 UP=0 BIOMES=0000000010100
+#=GS MGYP000660499351/22-69   DE [subseq from] PL=00 UP=0 BIOMES=1000000000000
+#=GS MGYP000054740637/2-50    DE [subseq from] PL=00 UP=0 BIOMES=0000000010100
+#=GS MGYP000111717601/1-44    DE [subseq from] PL=00 UP=0 BIOMES=0000000011000
+#=GS MGYP000888755554/1-44    DE [subseq from] PL=00 UP=0 BIOMES=0000000011000
+#=GS MGYP000294730968/1-44    DE [subseq from] PL=00 UP=0 BIOMES=0000000010100
+#=GS MGYP000492638681/46-75   DE [subseq from] PL=00 UP=0 BIOMES=0000000000001
+#=GS MGYP001120896613/151-179 DE [subseq from] PL=01 UP=0 BIOMES=0101000000000
+#=GS MGYP000299282490/49-75   DE [subseq from] PL=00 UP=0 BIOMES=0000101000000
+#=GS MGYP000665431927/41-61   DE [subseq from] PL=10 UP=0 BIOMES=0110000000000
+#=GS MGYP000236921234/89-111  DE [subseq from] PL=01 UP=0 BIOMES=0110000000000
+#=GS MGYP000139113544/297-357 DE [subseq from] PL=01 UP=0 BIOMES=0000000011000
+#=GS MGYP000139113544/476-542 DE [subseq from] PL=01 UP=0 BIOMES=0000000011000
+
+query                            GSSGSSGMEGPLNLAHQQSRRADRLLAAGKYEEAISCHRKATTYLSEAMKLTESEQAHLSLELQRDSHMKQLLLIQERWKRA-KREERLKAHSGPSSG
+MGYP000613015979/52-138          -----KVMEGPLNLAHQQSRRADRLLAAGKYEEAISCHKKAAAYLSEAMKLTQSEQAHLSLELQRDSHMKQLLLIQERWKRA-QREERLKAQQ-----
+MGYP000356782790/15-100          ------VMEGPLNLAHQQSRRADRLLAAGKYEEAISCHKKAAAYLSEAMKLTQSEQAHLSLELQRDSHMKQLLLIQERWKRA-QGEARLKAQQ-----
+MGYP000745946800/67-150          ------VMEGPLNLAHQQSRRADRLLAAGKYEEAISCHKKAAAYLSEAMKLTQSEQARLSLELQRDSHMKQLLLIQERWKRA-QREERLKA-------
+MGYP000365627167/34-120          -----EVMEGPLNLAHQQSRRADRLLAAGKYEEAISCHKKAAVYLSEAMKLTQSKQAHLSLELQRDSHMKQLLLIQERWKRA-QGEARLKAQQ-----
+MGYP000326981611/4-88            -------MEGPLNLAHQQSRRADRLLAAGKYEEAISCHKKAAAYLSEAMKLTQSEQARLSLELQRDSHMKQLLLIQERWKRP-QHEERLKAQQ-----
+MGYP000438079158/44-95           -----EVMEGPLNLAHQQSRRADHLLAAGKYEEAISCHKKAAVYLSEAMKLTQSEQV-----------------------------------------
+MGYP000660499351/22-69           --------NGSLNLAHQQSRRADRLLAAGKYEEAISCHKKAAAYLYEAMKLTQSEQ------------------------------------------
+MGYP000054740637/2-50            -------------------------------------------YLSEAMKLTQSKQAHLSLELQRDSHMKQLLLIQERWKRA-QGEARLKAQQ-----
+MGYP000111717601/1-44            ------------------------------------------------MKLTQSEQAHLSLELQRDSHMKQLLLIQERWKRA-QREERLKAQQ-----
+MGYP000888755554/1-44            ------------------------------------------------MKLTQSEQARLSLELQRDSHMKQLLLIQERWKRA-QREERLKAQQ-----
+MGYP000294730968/1-44            ------------------------------------------------MKLTQSKQAHLSLELQRDSHMKQLLLIQERWKRP-QHEERLKAQQ-----
+MGYP000492638681/46-75           ------------NNAKFYSRLAATLSALEKYEEAIDCYQKAI--------------------------------------------------------
+MGYP001120896613/151-179         -------------AAHVWNSKGDALANLGKYEEAIECYDKAI--------------------------------------------------------
+MGYP000299282490/49-75           ---------------YLLNKKGDNLSRLGKFEEAIECYDKAI--------------------------------------------------------
+MGYP000665431927/41-61           -----------------------ILQALGKYEEAIACYDKVITF------------------------------------------------------
+MGYP000236921234/89-111          ---------------------GKILEALGKYEEAIACYDKVITF------------------------------------------------------
+MGYP000139113544/297-357         ----------------REYQKALKLMTDEKYEEAIKAFEVLNNYSDSATKISECNTAILEREYQKAL--K--LMMDEKYEE-----------------
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+#=GC RF                          xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxx
+//