Multiple sequence alignment

The -in_msa psiblast option provides a way to jump start psiblast from a master-slave multiple sequence alignment computed outside psiblast. The multiple sequence alignment must contain the query sequence as one of its sequences, but it need not be the first sequence. The multiple sequence alignment must be specified in a format that is derived from Clustal, but without some headers and trailers (see example below).

The rules are also described by the following words. Suppose the multiple sequence alignment has N sequences. It may be presented in one or more blocks, where each block presents a range of columns from the multiple sequence alignment. E.g., the first block might have columns 1-60, the second block might have columns 61-95, the third block might have columns 96-128. Each block should have N rows, one row per sequence. The sequences should be in the same order in every block. Blocks are separated by one or more black lines. Within a block there are no blank lines, and each line consists of one sequence identifier followed by some whitespace followed by characters (and gaps) for that sequence in the multiple sequence alignment. In each column, all letters must be in upper case, or all letters must be in lower case.

# Example multiple sequence alignment file
 align1
------
26SPS9_Hs     IHAAEEKDWKTAYSYFYEAFEGYdsidspkaitslkymllckimlntpedvqalvsgkla
F57B9_Ce      LHAADEKDFKTAFSYFYEAFEGYdsvdekvsaltalkymllckvmldlpdevnsllsakl
YDL097c_Sc    ILHCEDKDYKTAFSYFFESFESYhnltthnsyekacqvlkymllskimlnliddvkniln
YMJ5_Ce       LYSAEERDYKTSFSYFYEAFEGFasigdkinatsalkymilckimlneteqlagllaake
FUS6_ARATH    KNYIRTRDYCTTTKHIIHMCMNAilvsiemgqfthvtsyvnkaeqnpetlepmvnaklrc
COS41.8_Ci    SLDYKLKTYLTIARLYLEDEDPVqaemyinrasllqnetadeqlqihykvcyarvldyrr
644879        KCYSRARDYCTSAKHVINMCLNVikvsvylqnwshvlsyvskaestpeiaeqrgerdsqt
YPR108w_Sc    IHCLAVRNFKEAAKLLVDSLATFtsieltsyesiatyasvtglftlertdlkskvidspe
eif-3p110_Hs  SKAMKMGDWKTCHSFIINEKMNGkvw----------------------------------
T23D8.4_Ce    SKAMLNGDWKKCQDYIVNDKMNQkvw----------------------------------
YD95_Sp       IYLMSIRNFSGAADLLLDCMSTFsstellpyydvvryavisgaisldrvdvktkivdspe
KIAA0107_Hs   LYCVAIRDFKQAAELFLDTVSTFtsyelmdyktfvtytvyvsmialerpdlrekvikgae
F49C12.8_Hs   LYRMSVRDFAGAADLFLEAVPTFgsyelmtyenlilytvitttfaldrpdlrtkvircne
Int-6_Mm      KFQYECGNYSGAAEYLYFFRVLVpatdrnalsslwgklaseilmqnwdaamedltrlket

26SPS9_Hs     lryagrqtealkcvaqasknrsladfekaltdy---------------------------
F57B9_Ce      alkyngsdldamkaiaaaaqkrslkdfqvafgsf--------------------------
YDL097c_Sc    akytketyqsrgidamkavaeaynnrslldfntalkqy----------------------
YMJ5_Ce       ivayqkspriiairsmadafrkrslkdfvkalaeh-------------------------
FUS6_ARATH    asglahlelkkyklaarkfldvnpelgnsyneviapqdiatygglcalasfdrselkqkv
COS41.8_Ci    kfleaaqrynelsyksaiheteqtkalekalncailapagqqrsrmlatlfkdercqllp
644879        qailtklkcaaglaelaarkykqaakclllasfdhcdfpellspsnvaiygglcalatfd
YPR108w_Sc    llslisttaalqsissltislyasdyasyfpyllety-----------------------
eif-3p110_Hs  ------------------------------------------------------------
T23D8.4_Ce    ------------------------------------------------------------
YD95_Sp       vlavlpqnesmssleacinslylcdysgffrtladve-----------------------
KIAA0107_Hs   ilevlhslpavrqylfslyecrysvffqslavv---------------------------
F49C12.8_Hs   vqeqltggglngtlipvreylesyydchydrffiqlaale--------------------
Int-6_Mm      idnnsvssplqslqqrtwlihwslfvffnhpkgrdniidlflyqpqylnaiqtmcphilr

26SPS9_Hs     ------------------------------------------------------------
F57B9_Ce      ------------------------------------------------------------
YDL097c_Sc    ------------------------------------------------------------
YMJ5_Ce       ------------------------------------------------------------
FUS6_ARATH    idninfrnflelvpdvrelindfyssryascleylasl----------------------
COS41.8_Ci    sfgilekmfldriiksdemeefar------------------------------------
644879        rqelqrnvissssfklflelepqvrdiifkfyeskyasclkmldem--------------
YPR108w_Sc    ------------------------------------------------------------
eif-3p110_Hs  ------------------------------------------------------------
T23D8.4_Ce    ------------------------------------------------------------
YD95_Sp       ------------------------------------------------------------
KIAA0107_Hs   ------------------------------------------------------------
F49C12.8_Hs   ------------------------------------------------------------
Int-6_Mm      ylttavitnkdvrkrrqvlkdlvkviqqesytykdpitefveclyvnfdfdgaqkklrec

26SPS9_Hs     RAELRDDPIISTHLAKLYDNLLEQNLIRVIEPFSRVQIEHISSLIKLSKADVERKLSQMI
F57B9_Ce      PQELQMDPVVRKHFHSLSERMLEKDLCRIIEPYSFVQIEHVAQQIGIDRSKVEKKLSQMI
YDL097c_Sc    EKELMGDELTRSHFNALYDTLLESNLCKIIEPFECVEISHISKIIGLDTQQVEGKLSQMI
YMJ5_Ce       KIELVEDKVVAVHSQNLERNMLEKEISRVIEPYSEIELSYIARVIGMTVPPVERAIARMI
FUS6_ARATH    KSNLLLDIHLHDHVDTLYDQIRKKALIQYTLPFVSVDLSRMADAFKTSVSGLEKELEALI
COS41.8_Ci    QLMPHQKAITADGSNILHRAVTEHNLLSASKLYNNIRFTELGALLEIPHQMAEKVASQMI
644879        KDNLLLDMYLAPHVRTLYTQIRNRALIQYFSPYVSADMHRMAAAFNTTVAALEDELTQLI
YPR108w_Sc    ANVLIPCKYLNRHADFFVREMRRKVYAQLLESYKTLSLKSMASAFGVSVAFLDNDLGKFI
eif-3p110_Hs  DLFPEADKVRTMLVRKIQEESLRTYLFTYSSVYDSISMETLSDMFELDLPTVHSIISKMI
T23D8.4_Ce    NLFHNAETVKGMVVRRIQEESLRTYLLTYSTVYATVSLKKLADLFELSKKDVHSIISKMI
YD95_Sp       VNHLKCDQFLVAHYRYYVREMRRRAYAQLLESYRALSIDSMAASFGVSVDYIDRDLASFI
KIAA0107_Hs   EQEMKKDWLFAPHYRYYVREMRIHAYSQLLESYRSLTLGYMAEAFGVGVEFIDQELSRFI
F49C12.8_Hs   SERFKFDRYLSPHFNYYSRGMRHRAYEQFLTPYKTVRIDMMAKDFGVSRAFIDRELHRLI
Int-6_Mm      ESVLVNDFFLVACLEDFIENARLFIFETFCRIHQCISINMLADKLNMTPEEAERWIVNLI

26SPS9_Hs     LDKKFHGILDQGEGVLIIFDEPP
F57B9_Ce      LDQKLSGSLDQGEGMLIVFEIAV
YDL097c_Sc    LDKIFYGVLDQGNGWLYVYETPN
YMJ5_Ce       LDKKLMGSIDQHGDTVVVYPKAD
FUS6_ARATH    TDNQIQARIDSHNKILYARHADQ
COS41.8_Ci    CESRMKGHIDQIDGIVFFERRET
644879        LEGLISARVDSHSKILYARDVDQ
YPR108w_Sc    PNKQLNCVIDRVNGIVETNRPDN
eif-3p110_Hs  INEELMASLDQPTQTVVMHRTEP
T23D8.4_Ce    IQEELSATLDEPTDCLIMHRVEP
YD95_Sp       PDNKLNCVIDRVNGVVFTNRPDE
KIAA0107_Hs   AAGRLHCKIDKVNEIVETNRPDS
F49C12.8_Hs   ATGQLQCRIDAVNGVIEVNHRDS
Int-6_Mm      RNARLDAKIDSKLGHVVMGNNAV