AB Map features2alignment
There are very few alignment programs that will read sequence formats with rich annotations, let alone retain those annotations after the alignment is complete. This tool allows you to map annotations from a genbank or embl file onto an alignment generated from the same sequences. Pass the alignment file into AlignBuddy normally, and then include one or more sequence files after the flag. Records with a matching ID will be mapped.
Provide the path to at least one file with annotated records that match those in your alignment. Extra records are ignored, so it's okay to supply a larger set of annotated sequences; only those with matching IDs in the alignment file will be mapped.
3 465
Mle-Panxα9 ---MLDILSK FKGVTPFKGI TIDDGWDQLN RSFMFVLLVV MGTTVTVRQY
Mle-Panxα1 MYWIFEICQE IKRAQSCRKF AIDGPFDWTN RIIMPTLMVI CCFLQTFTFM
Mle-Panxα3 M-LLLGSLGT IKNLSIFKDL SLDDWLDQMN RTFMFLLLCF MGTIVAVSQY
TGSVISCDGF KKFGSTFAED YCWTQGLYTV LEGYDQPSQN IPYPGLLPDE
FGSNISCIGF EKLERNFVEE YCWTQGIYTS KAAYNMP-LH TPYPGIAPC-
TGKNISCDGF TKFGEDFSQD YCWTQGLYTI KEAYDLPESQ IPYPGIIPEN
APPCTP-VRL KDGTRLKCPD PDQLLSPTRI SHLWYQWVPF YFWLAAAAFF
VPEYDPV--- -TQKYWLPCG ---VEEEDKA YHLWYQWVPF YFLAVAVGYY
VPACRE-HAL KNGGKIVCPP EDQVKPLTRA RHLWYQWIPF YFWVIAPVFY
MPYLLYKNFG MGDIKPLVRL LHNPVESDQE --LKKMTDKA ATWLFYKFDL
LPFLILKGSK LHQVKPLITY LMNQRNLETD --PNHLVGKL SHWIFRQLVY
LPYMFVKRMG LDRMKPLLKI MSDYYHCTTE TPSEEIIVKC ADWVYNSIVD
YMSEQSLLAS LTRKH-GLGL SMVFVKILYA AVSFGCFLLT AEMFSIGDFK
SRFAATSTIR MYWHDWGLVL LVCSVKILYL TVSLIHLFAT AKMFHIGNWF
RLSEGSSWTS WRNRH-GLGL AVLVSKFMYL GGSVLVMMMT TLMFQVGDFK
TYGSEWIKKL KLEDNLATEE KDKLFPKMVA CEVKRWGASG IEEEQGMCVL
TYGIMFARR- --SNSHTTHV KDVFFPKMVA CKIETWSFTG KNHLHGMCVL
TYGIEWLRQF PNPENYSTSV KHKLFPKMVA CEIKRWGTTG LEEENGMCVL
APNVINQYLF LILWFCLVFV MFCNIVSIFA SLIKLLFTYG SYRRLLSTA-
ALNVMNQYLF LIVWYVNVII IFLNSISCIY TIVKFCSPNI VHHRIVNSS-
APNVIYQYIF LIMWFALAIT ICTNFGNIFF YLFKLTATRY TYNKLVATGH
FLRDDSAIKH MYFNVGSSGR LILHVLANNT APRVFEDILL TLAPKLI---
SLDDHHDFTR MFGYVGPSGR IILAKMSEHM PGYMLKQVAK KVTEKID---
FSHKHPGWKF MYYRIGTSGR VLLNIVAQNT NPIIFGAIME KLTPSVIKHL
QRKLRGNGKA L*-------- ---------- ---------- ----------
IENEKNRGRA PTIKFTKVNG QPSELARQPL MHLNALMLGM VPQNLPEPKI
RIGHVPGEYL T--------- ---------- -DPA*----- ----------
---------- -----
QNIQRSQKKV RFLV*
---------- -----
LOCUS Mle-Panxα9 401 aa UNA 02-JAN-2015
DEFINITION cDNA - ML47742a.
ACCESSION Mle-Panxα9
VERSION Mle-Panxα9
KEYWORDS .
SOURCE
ORGANISM .
.
FEATURES Location/Qualifiers
CDS 1..401
/created_by="User"
/label="ML47742a"
/modified_by="User"
splice_donor 13..15
/created_by="User"
/label="47%"
TMD1 27..47
TMD2 130..150
TMD3 214..234
TMD4 301..331
ORIGIN
1 mldilskfkg vtpfkgitid dgwdqlnrsf mfvllvvmgt tvtvrqytgs viscdgfkkf
61 gstfaedycw tqglytvleg ydqpsqnipy pgllpdeapp ctpvrlkdgt rlkcpdpdql
121 lsptrishlw yqwvpfyfwl aaaaffmpyl lyknfgmgdi kplvrllhnp vesdqelkkm
181 tdkaatwlfy kfdlymseqs llasltrkhg lglsmvfvki lyaavsfgcf lltaemfsig
241 dfktygsewi kklklednla teekdklfpk mvacevkrwg asgieeeqgm cvlapnvinq
301 ylflilwfcl vfvmfcnivs ifaslikllf tygsyrrlls taflrddsai khmyfnvgss
361 grlilhvlan ntaprvfedi lltlapkliq rklrgngkal *
//
LOCUS Mle-Panxα1 447 aa UNA 02-JAN-2015
DEFINITION cDNA - ML078817.
ACCESSION Mle-Panxα1
VERSION Mle-Panxα1
KEYWORDS .
SOURCE
ORGANISM .
.
FEATURES Location/Qualifiers
CDS 1..447
/created_by="User"
/label="ML078817"
TMD1 31..51
TMD2 125..145
TMD3 209..229
TMD4 291..321
ORIGIN
1 mywifeicqe ikraqscrkf aidgpfdwtn riimptlmvi ccflqtftfm fgsniscigf
61 eklernfvee ycwtqgiyts kaaynmplht pypgiapcvp eydpvtqkyw lpcgveeedk
121 ayhlwyqwvp fyflavavgy ylpflilkgs klhqvkplit ylmnqrnlet dpnhlvgkls
181 hwifrqlvys rfaatstirm ywhdwglvll vcsvkilylt vslihlfata kmfhignwft
241 ygimfarrsn shtthvkdvf fpkmvackie twsftgknhl hgmcvlalnv mnqylflivw
301 yvnviiifln sisciytivk fcspnivhhr ivnssslddh hdftrmfgyv gpsgriilak
361 msehmpgyml kqvakkvtek idieneknrg raptikftkv ngqpselarq plmhlnalml
421 gmvpqnlpep kiqniqrsqk kvrflv*
//
LOCUS Mle-Panxα3 412 aa UNA 02-JAN-2015
DEFINITION cDNA - ML036514a.
ACCESSION Mle-Panxα3
VERSION Mle-Panxα3
KEYWORDS .
SOURCE
ORGANISM .
.
FEATURES Location/Qualifiers
CDS 1..412
/created_by="User"
/label="ML036514a"
/modified_by="User"
TMD1 29..49
TMD2 132..152
TMD3 218..238
TMD4 302..332
ORIGIN
1 mlllgslgti knlsifkdls lddwldqmnr tfmflllcfm gtivavsqyt gkniscdgft
61 kfgedfsqdy cwtqglytik eaydlpesqi pypgiipenv pacrehalkn ggkivcpped
121 qvkpltrarh lwyqwipfyf wviapvfylp ymfvkrmgld rmkpllkims dyyhcttetp
181 seeiivkcad wvynsivdrl segsswtswr nrhglglavl vskfmylggs vlvmmmttlm
241 fqvgdfktyg iewlrqfpnp enystsvkhk lfpkmvacei krwgttglee engmcvlapn
301 viyqyiflim wfalaitict nfgniffylf kltatrytyn klvatghfsh khpgwkfmyy
361 rigtsgrvll nivaqntnpi ifgaimeklt psvikhlrig hvpgeyltdp a*
//
$: alb Mle-Panx.phy -mf2a Mle-Panx.gb
LOCUS Mle-Panxα9 465 aa UNK 01-JAN-1980
DEFINITION Mle-Panxα9
ACCESSION Mle-Panxα9
VERSION Mle-Panxα9
KEYWORDS .
SOURCE .
ORGANISM .
.
FEATURES Location/Qualifiers
CDS 4..411
/created_by="User"
/label="ML47742a"
/modified_by="User"
splice_donor 16..18
/created_by="User"
/label="47%"
TMD1 30..50
TMD2 134..154
TMD3 221..241
TMD4 308..338
ORIGIN
1 ---mldilsk fkgvtpfkgi tiddgwdqln rsfmfvllvv mgttvtvrqy tgsviscdgf
61 kkfgstfaed ycwtqglytv legydqpsqn ipypgllpde appctp-vrl kdgtrlkcpd
121 pdqllsptri shlwyqwvpf yfwlaaaaff mpyllyknfg mgdikplvrl lhnpvesdqe
181 --lkkmtdka atwlfykfdl ymseqsllas ltrkh-glgl smvfvkilya avsfgcfllt
241 aemfsigdfk tygsewikkl klednlatee kdklfpkmva cevkrwgasg ieeeqgmcvl
301 apnvinqylf lilwfclvfv mfcnivsifa slikllftyg syrrllsta- flrddsaikh
361 myfnvgssgr lilhvlannt aprvfedill tlapkli--- qrklrgngka l*--------
421 ---------- ---------- ---------- ---------- -----
//
LOCUS Mle-Panxα1 465 aa UNK 01-JAN-1980
DEFINITION Mle-Panxα1
ACCESSION Mle-Panxα1
VERSION Mle-Panxα1
KEYWORDS .
SOURCE .
ORGANISM .
.
FEATURES Location/Qualifiers
CDS 1..464
/created_by="User"
/label="ML078817"
TMD1 31..51
TMD2 134..154
TMD3 220..240
TMD4 305..335
ORIGIN
1 mywifeicqe ikraqscrkf aidgpfdwtn riimptlmvi ccflqtftfm fgsniscigf
61 eklernfvee ycwtqgiyts kaaynmp-lh tpypgiapc- vpeydpv--- -tqkywlpcg
121 ---veeedka yhlwyqwvpf yflavavgyy lpflilkgsk lhqvkplity lmnqrnletd
181 --pnhlvgkl shwifrqlvy srfaatstir mywhdwglvl lvcsvkilyl tvslihlfat
241 akmfhignwf tygimfarr- --snshtthv kdvffpkmva ckietwsftg knhlhgmcvl
301 alnvmnqylf livwyvnvii iflnsisciy tivkfcspni vhhrivnss- slddhhdftr
361 mfgyvgpsgr iilakmsehm pgymlkqvak kvtekid--- ieneknrgra ptikftkvng
421 qpselarqpl mhlnalmlgm vpqnlpepki qniqrsqkkv rflv*
//
LOCUS Mle-Panxα3 465 aa UNK 01-JAN-1980
DEFINITION Mle-Panxα3
ACCESSION Mle-Panxα3
VERSION Mle-Panxα3
KEYWORDS .
SOURCE .
ORGANISM .
.
FEATURES Location/Qualifiers
CDS 1..434
/created_by="User"
/label="ML036514a"
/modified_by="User"
TMD1 30..50
TMD2 134..154
TMD3 221..241
TMD4 305..335
ORIGIN
1 m-lllgslgt iknlsifkdl slddwldqmn rtfmflllcf mgtivavsqy tgkniscdgf
61 tkfgedfsqd ycwtqglyti keaydlpesq ipypgiipen vpacre-hal knggkivcpp
121 edqvkpltra rhlwyqwipf yfwviapvfy lpymfvkrmg ldrmkpllki msdyyhctte
181 tpseeiivkc adwvynsivd rlsegsswts wrnrh-glgl avlvskfmyl ggsvlvmmmt
241 tlmfqvgdfk tygiewlrqf pnpenystsv khklfpkmva ceikrwgttg leeengmcvl
301 apnviyqyif limwfalait ictnfgniff ylfkltatry tynklvatgh fshkhpgwkf
361 myyrigtsgr vllnivaqnt npiifgaime kltpsvikhl righvpgeyl t---------
421 ---------- -dpa*----- ---------- ---------- -----
//
